2016_WGS_DataPrep.html

<!DOCTYPE html>
<html>
<head><meta charset="utf-8" />


<title>2016_WGS_DataPrep</title>

<style type="text/css">
    /*!
*
* Twitter Bootstrap
*
*/
/*!
 * Bootstrap v3.3.7 (http://getbootstrap.com)
 * Copyright 2011-2016 Twitter, Inc.
 * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
 */
/*! normalize.css v3.0.3 | MIT License | github.com/necolas/normalize.css */
html {
  font-family: sans-serif;
  -ms-text-size-adjust: 100%;
  -webkit-text-size-adjust: 100%;
}
body {
  margin: 0;
}
article,
aside,
details,
figcaption,
figure,
footer,
header,
hgroup,
main,
menu,
nav,
section,
summary {
  display: block;
}
audio,
canvas,
progress,
video {
  display: inline-block;
  vertical-align: baseline;
}
audio:not([controls]) {
  display: none;
  height: 0;
}
[hidden],
template {
  display: none;
}
a {
  background-color: transparent;
}
a:active,
a:hover {
  outline: 0;
}
abbr[title] {
  border-bottom: 1px dotted;
}
b,
strong {
  font-weight: bold;
}
dfn {
  font-style: italic;
}
h1 {
  font-size: 2em;
  margin: 0.67em 0;
}
mark {
  background: #ff0;
  color: #000;
}
small {
  font-size: 80%;
}
sub,
sup {
  font-size: 75%;
  line-height: 0;
  position: relative;
  vertical-align: baseline;
}
sup {
  top: -0.5em;
}
sub {
  bottom: -0.25em;
}
img {
  border: 0;
}
svg:not(:root) {
  overflow: hidden;
}
figure {
  margin: 1em 40px;
}
hr {
  box-sizing: content-box;
  height: 0;
}
pre {
  overflow: auto;
}
code,
kbd,
pre,
samp {
  font-family: monospace, monospace;
  font-size: 1em;
}
button,
input,
optgroup,
select,
textarea {
  color: inherit;
  font: inherit;
  margin: 0;
}
button {
  overflow: visible;
}
button,
select {
  text-transform: none;
}
button,
html input[type="button"],
input[type="reset"],
input[type="submit"] {
  -webkit-appearance: button;
  cursor: pointer;
}
button[disabled],
html input[disabled] {
  cursor: default;
}
button::-moz-focus-inner,
input::-moz-focus-inner {
  border: 0;
  padding: 0;
}
input {
  line-height: normal;
}
input[type="checkbox"],
input[type="radio"] {
  box-sizing: border-box;
  padding: 0;
}
input[type="number"]::-webkit-inner-spin-button,
input[type="number"]::-webkit-outer-spin-button {
  height: auto;
}
input[type="search"] {
  -webkit-appearance: textfield;
  box-sizing: content-box;
}
input[type="search"]::-webkit-search-cancel-button,
input[type="search"]::-webkit-search-decoration {
  -webkit-appearance: none;
}
fieldset {
  border: 1px solid #c0c0c0;
  margin: 0 2px;
  padding: 0.35em 0.625em 0.75em;
}
legend {
  border: 0;
  padding: 0;
}
textarea {
  overflow: auto;
}
optgroup {
  font-weight: bold;
}
table {
  border-collapse: collapse;
  border-spacing: 0;
}
td,
th {
  padding: 0;
}
/*! Source: https://github.com/h5bp/html5-boilerplate/blob/master/src/css/main.css */
@media print {
  *,
  *:before,
  *:after {
    background: transparent !important;
    box-shadow: none !important;
    text-shadow: none !important;
  }
  a,
  a:visited {
    text-decoration: underline;
  }
  a[href]:after {
    content: " (" attr(href) ")";
  }
  abbr[title]:after {
    content: " (" attr(title) ")";
  }
  a[href^="#"]:after,
  a[href^="javascript:"]:after {
    content: "";
  }
  pre,
  blockquote {
    border: 1px solid #999;
    page-break-inside: avoid;
  }
  thead {
    display: table-header-group;
  }
  tr,
  img {
    page-break-inside: avoid;
  }
  img {
    max-width: 100% !important;
  }
  p,
  h2,
  h3 {
    orphans: 3;
    widows: 3;
  }
  h2,
  h3 {
    page-break-after: avoid;
  }
  .navbar {
    display: none;
  }
  .btn > .caret,
  .dropup > .btn > .caret {
    border-top-color: #000 !important;
  }
  .label {
    border: 1px solid #000;
  }
  .table {
    border-collapse: collapse !important;
  }
  .table td,
  .table th {
    background-color: #fff !important;
  }
  .table-bordered th,
  .table-bordered td {
    border: 1px solid #ddd !important;
  }
}
@font-face {
  font-family: 'Glyphicons Halflings';
  src: url('../components/bootstrap/fonts/glyphicons-halflings-regular.eot');
  src: url('../components/bootstrap/fonts/glyphicons-halflings-regular.eot?#iefix') format('embedded-opentype'), url('../components/bootstrap/fonts/glyphicons-halflings-regular.woff2') format('woff2'), url('../components/bootstrap/fonts/glyphicons-halflings-regular.woff') format('woff'), url('../components/bootstrap/fonts/glyphicons-halflings-regular.ttf') format('truetype'), url('../components/bootstrap/fonts/glyphicons-halflings-regular.svg#glyphicons_halflingsregular') format('svg');
}
.glyphicon {
  position: relative;
  top: 1px;
  display: inline-block;
  font-family: 'Glyphicons Halflings';
  font-style: normal;
  font-weight: normal;
  line-height: 1;
  -webkit-font-smoothing: antialiased;
  -moz-osx-font-smoothing: grayscale;
}
.glyphicon-asterisk:before {
  content: "\002a";
}
.glyphicon-plus:before {
  content: "\002b";
}
.glyphicon-euro:before,
.glyphicon-eur:before {
  content: "\20ac";
}
.glyphicon-minus:before {
  content: "\2212";
}
.glyphicon-cloud:before {
  content: "\2601";
}
.glyphicon-envelope:before {
  content: "\2709";
}
.glyphicon-pencil:before {
  content: "\270f";
}
.glyphicon-glass:before {
  content: "\e001";
}
.glyphicon-music:before {
  content: "\e002";
}
.glyphicon-search:before {
  content: "\e003";
}
.glyphicon-heart:before {
  content: "\e005";
}
.glyphicon-star:before {
  content: "\e006";
}
.glyphicon-star-empty:before {
  content: "\e007";
}
.glyphicon-user:before {
  content: "\e008";
}
.glyphicon-film:before {
  content: "\e009";
}
.glyphicon-th-large:before {
  content: "\e010";
}
.glyphicon-th:before {
  content: "\e011";
}
.glyphicon-th-list:before {
  content: "\e012";
}
.glyphicon-ok:before {
  content: "\e013";
}
.glyphicon-remove:before {
  content: "\e014";
}
.glyphicon-zoom-in:before {
  content: "\e015";
}
.glyphicon-zoom-out:before {
  content: "\e016";
}
.glyphicon-off:before {
  content: "\e017";
}
.glyphicon-signal:before {
  content: "\e018";
}
.glyphicon-cog:before {
  content: "\e019";
}
.glyphicon-trash:before {
  content: "\e020";
}
.glyphicon-home:before {
  content: "\e021";
}
.glyphicon-file:before {
  content: "\e022";
}
.glyphicon-time:before {
  content: "\e023";
}
.glyphicon-road:before {
  content: "\e024";
}
.glyphicon-download-alt:before {
  content: "\e025";
}
.glyphicon-download:before {
  content: "\e026";
}
.glyphicon-upload:before {
  content: "\e027";
}
.glyphicon-inbox:before {
  content: "\e028";
}
.glyphicon-play-circle:before {
  content: "\e029";
}
.glyphicon-repeat:before {
  content: "\e030";
}
.glyphicon-refresh:before {
  content: "\e031";
}
.glyphicon-list-alt:before {
  content: "\e032";
}
.glyphicon-lock:before {
  content: "\e033";
}
.glyphicon-flag:before {
  content: "\e034";
}
.glyphicon-headphones:before {
  content: "\e035";
}
.glyphicon-volume-off:before {
  content: "\e036";
}
.glyphicon-volume-down:before {
  content: "\e037";
}
.glyphicon-volume-up:before {
  content: "\e038";
}
.glyphicon-qrcode:before {
  content: "\e039";
}
.glyphicon-barcode:before {
  content: "\e040";
}
.glyphicon-tag:before {
  content: "\e041";
}
.glyphicon-tags:before {
  content: "\e042";
}
.glyphicon-book:before {
  content: "\e043";
}
.glyphicon-bookmark:before {
  content: "\e044";
}
.glyphicon-print:before {
  content: "\e045";
}
.glyphicon-camera:before {
  content: "\e046";
}
.glyphicon-font:before {
  content: "\e047";
}
.glyphicon-bold:before {
  content: "\e048";
}
.glyphicon-italic:before {
  content: "\e049";
}
.glyphicon-text-height:before {
  content: "\e050";
}
.glyphicon-text-width:before {
  content: "\e051";
}
.glyphicon-align-left:before {
  content: "\e052";
}
.glyphicon-align-center:before {
  content: "\e053";
}
.glyphicon-align-right:before {
  content: "\e054";
}
.glyphicon-align-justify:before {
  content: "\e055";
}
.glyphicon-list:before {
  content: "\e056";
}
.glyphicon-indent-left:before {
  content: "\e057";
}
.glyphicon-indent-right:before {
  content: "\e058";
}
.glyphicon-facetime-video:before {
  content: "\e059";
}
.glyphicon-picture:before {
  content: "\e060";
}
.glyphicon-map-marker:before {
  content: "\e062";
}
.glyphicon-adjust:before {
  content: "\e063";
}
.glyphicon-tint:before {
  content: "\e064";
}
.glyphicon-edit:before {
  content: "\e065";
}
.glyphicon-share:before {
  content: "\e066";
}
.glyphicon-check:before {
  content: "\e067";
}
.glyphicon-move:before {
  content: "\e068";
}
.glyphicon-step-backward:before {
  content: "\e069";
}
.glyphicon-fast-backward:before {
  content: "\e070";
}
.glyphicon-backward:before {
  content: "\e071";
}
.glyphicon-play:before {
  content: "\e072";
}
.glyphicon-pause:before {
  content: "\e073";
}
.glyphicon-stop:before {
  content: "\e074";
}
.glyphicon-forward:before {
  content: "\e075";
}
.glyphicon-fast-forward:before {
  content: "\e076";
}
.glyphicon-step-forward:before {
  content: "\e077";
}
.glyphicon-eject:before {
  content: "\e078";
}
.glyphicon-chevron-left:before {
  content: "\e079";
}
.glyphicon-chevron-right:before {
  content: "\e080";
}
.glyphicon-plus-sign:before {
  content: "\e081";
}
.glyphicon-minus-sign:before {
  content: "\e082";
}
.glyphicon-remove-sign:before {
  content: "\e083";
}
.glyphicon-ok-sign:before {
  content: "\e084";
}
.glyphicon-question-sign:before {
  content: "\e085";
}
.glyphicon-info-sign:before {
  content: "\e086";
}
.glyphicon-screenshot:before {
  content: "\e087";
}
.glyphicon-remove-circle:before {
  content: "\e088";
}
.glyphicon-ok-circle:before {
  content: "\e089";
}
.glyphicon-ban-circle:before {
  content: "\e090";
}
.glyphicon-arrow-left:before {
  content: "\e091";
}
.glyphicon-arrow-right:before {
  content: "\e092";
}
.glyphicon-arrow-up:before {
  content: "\e093";
}
.glyphicon-arrow-down:before {
  content: "\e094";
}
.glyphicon-share-alt:before {
  content: "\e095";
}
.glyphicon-resize-full:before {
  content: "\e096";
}
.glyphicon-resize-small:before {
  content: "\e097";
}
.glyphicon-exclamation-sign:before {
  content: "\e101";
}
.glyphicon-gift:before {
  content: "\e102";
}
.glyphicon-leaf:before {
  content: "\e103";
}
.glyphicon-fire:before {
  content: "\e104";
}
.glyphicon-eye-open:before {
  content: "\e105";
}
.glyphicon-eye-close:before {
  content: "\e106";
}
.glyphicon-warning-sign:before {
  content: "\e107";
}
.glyphicon-plane:before {
  content: "\e108";
}
.glyphicon-calendar:before {
  content: "\e109";
}
.glyphicon-random:before {
  content: "\e110";
}
.glyphicon-comment:before {
  content: "\e111";
}
.glyphicon-magnet:before {
  content: "\e112";
}
.glyphicon-chevron-up:before {
  content: "\e113";
}
.glyphicon-chevron-down:before {
  content: "\e114";
}
.glyphicon-retweet:before {
  content: "\e115";
}
.glyphicon-shopping-cart:before {
  content: "\e116";
}
.glyphicon-folder-close:before {
  content: "\e117";
}
.glyphicon-folder-open:before {
  content: "\e118";
}
.glyphicon-resize-vertical:before {
  content: "\e119";
}
.glyphicon-resize-horizontal:before {
  content: "\e120";
}
.glyphicon-hdd:before {
  content: "\e121";
}
.glyphicon-bullhorn:before {
  content: "\e122";
}
.glyphicon-bell:before {
  content: "\e123";
}
.glyphicon-certificate:before {
  content: "\e124";
}
.glyphicon-thumbs-up:before {
  content: "\e125";
}
.glyphicon-thumbs-down:before {
  content: "\e126";
}
.glyphicon-hand-right:before {
  content: "\e127";
}
.glyphicon-hand-left:before {
  content: "\e128";
}
.glyphicon-hand-up:before {
  content: "\e129";
}
.glyphicon-hand-down:before {
  content: "\e130";
}
.glyphicon-circle-arrow-right:before {
  content: "\e131";
}
.glyphicon-circle-arrow-left:before {
  content: "\e132";
}
.glyphicon-circle-arrow-up:before {
  content: "\e133";
}
.glyphicon-circle-arrow-down:before {
  content: "\e134";
}
.glyphicon-globe:before {
  content: "\e135";
}
.glyphicon-wrench:before {
  content: "\e136";
}
.glyphicon-tasks:before {
  content: "\e137";
}
.glyphicon-filter:before {
  content: "\e138";
}
.glyphicon-briefcase:before {
  content: "\e139";
}
.glyphicon-fullscreen:before {
  content: "\e140";
}
.glyphicon-dashboard:before {
  content: "\e141";
}
.glyphicon-paperclip:before {
  content: "\e142";
}
.glyphicon-heart-empty:before {
  content: "\e143";
}
.glyphicon-link:before {
  content: "\e144";
}
.glyphicon-phone:before {
  content: "\e145";
}
.glyphicon-pushpin:before {
  content: "\e146";
}
.glyphicon-usd:before {
  content: "\e148";
}
.glyphicon-gbp:before {
  content: "\e149";
}
.glyphicon-sort:before {
  content: "\e150";
}
.glyphicon-sort-by-alphabet:before {
  content: "\e151";
}
.glyphicon-sort-by-alphabet-alt:before {
  content: "\e152";
}
.glyphicon-sort-by-order:before {
  content: "\e153";
}
.glyphicon-sort-by-order-alt:before {
  content: "\e154";
}
.glyphicon-sort-by-attributes:before {
  content: "\e155";
}
.glyphicon-sort-by-attributes-alt:before {
  content: "\e156";
}
.glyphicon-unchecked:before {
  content: "\e157";
}
.glyphicon-expand:before {
  content: "\e158";
}
.glyphicon-collapse-down:before {
  content: "\e159";
}
.glyphicon-collapse-up:before {
  content: "\e160";
}
.glyphicon-log-in:before {
  content: "\e161";
}
.glyphicon-flash:before {
  content: "\e162";
}
.glyphicon-log-out:before {
  content: "\e163";
}
.glyphicon-new-window:before {
  content: "\e164";
}
.glyphicon-record:before {
  content: "\e165";
}
.glyphicon-save:before {
  content: "\e166";
}
.glyphicon-open:before {
  content: "\e167";
}
.glyphicon-saved:before {
  content: "\e168";
}
.glyphicon-import:before {
  content: "\e169";
}
.glyphicon-export:before {
  content: "\e170";
}
.glyphicon-send:before {
  content: "\e171";
}
.glyphicon-floppy-disk:before {
  content: "\e172";
}
.glyphicon-floppy-saved:before {
  content: "\e173";
}
.glyphicon-floppy-remove:before {
  content: "\e174";
}
.glyphicon-floppy-save:before {
  content: "\e175";
}
.glyphicon-floppy-open:before {
  content: "\e176";
}
.glyphicon-credit-card:before {
  content: "\e177";
}
.glyphicon-transfer:before {
  content: "\e178";
}
.glyphicon-cutlery:before {
  content: "\e179";
}
.glyphicon-header:before {
  content: "\e180";
}
.glyphicon-compressed:before {
  content: "\e181";
}
.glyphicon-earphone:before {
  content: "\e182";
}
.glyphicon-phone-alt:before {
  content: "\e183";
}
.glyphicon-tower:before {
  content: "\e184";
}
.glyphicon-stats:before {
  content: "\e185";
}
.glyphicon-sd-video:before {
  content: "\e186";
}
.glyphicon-hd-video:before {
  content: "\e187";
}
.glyphicon-subtitles:before {
  content: "\e188";
}
.glyphicon-sound-stereo:before {
  content: "\e189";
}
.glyphicon-sound-dolby:before {
  content: "\e190";
}
.glyphicon-sound-5-1:before {
  content: "\e191";
}
.glyphicon-sound-6-1:before {
  content: "\e192";
}
.glyphicon-sound-7-1:before {
  content: "\e193";
}
.glyphicon-copyright-mark:before {
  content: "\e194";
}
.glyphicon-registration-mark:before {
  content: "\e195";
}
.glyphicon-cloud-download:before {
  content: "\e197";
}
.glyphicon-cloud-upload:before {
  content: "\e198";
}
.glyphicon-tree-conifer:before {
  content: "\e199";
}
.glyphicon-tree-deciduous:before {
  content: "\e200";
}
.glyphicon-cd:before {
  content: "\e201";
}
.glyphicon-save-file:before {
  content: "\e202";
}
.glyphicon-open-file:before {
  content: "\e203";
}
.glyphicon-level-up:before {
  content: "\e204";
}
.glyphicon-copy:before {
  content: "\e205";
}
.glyphicon-paste:before {
  content: "\e206";
}
.glyphicon-alert:before {
  content: "\e209";
}
.glyphicon-equalizer:before {
  content: "\e210";
}
.glyphicon-king:before {
  content: "\e211";
}
.glyphicon-queen:before {
  content: "\e212";
}
.glyphicon-pawn:before {
  content: "\e213";
}
.glyphicon-bishop:before {
  content: "\e214";
}
.glyphicon-knight:before {
  content: "\e215";
}
.glyphicon-baby-formula:before {
  content: "\e216";
}
.glyphicon-tent:before {
  content: "\26fa";
}
.glyphicon-blackboard:before {
  content: "\e218";
}
.glyphicon-bed:before {
  content: "\e219";
}
.glyphicon-apple:before {
  content: "\f8ff";
}
.glyphicon-erase:before {
  content: "\e221";
}
.glyphicon-hourglass:before {
  content: "\231b";
}
.glyphicon-lamp:before {
  content: "\e223";
}
.glyphicon-duplicate:before {
  content: "\e224";
}
.glyphicon-piggy-bank:before {
  content: "\e225";
}
.glyphicon-scissors:before {
  content: "\e226";
}
.glyphicon-bitcoin:before {
  content: "\e227";
}
.glyphicon-btc:before {
  content: "\e227";
}
.glyphicon-xbt:before {
  content: "\e227";
}
.glyphicon-yen:before {
  content: "\00a5";
}
.glyphicon-jpy:before {
  content: "\00a5";
}
.glyphicon-ruble:before {
  content: "\20bd";
}
.glyphicon-rub:before {
  content: "\20bd";
}
.glyphicon-scale:before {
  content: "\e230";
}
.glyphicon-ice-lolly:before {
  content: "\e231";
}
.glyphicon-ice-lolly-tasted:before {
  content: "\e232";
}
.glyphicon-education:before {
  content: "\e233";
}
.glyphicon-option-horizontal:before {
  content: "\e234";
}
.glyphicon-option-vertical:before {
  content: "\e235";
}
.glyphicon-menu-hamburger:before {
  content: "\e236";
}
.glyphicon-modal-window:before {
  content: "\e237";
}
.glyphicon-oil:before {
  content: "\e238";
}
.glyphicon-grain:before {
  content: "\e239";
}
.glyphicon-sunglasses:before {
  content: "\e240";
}
.glyphicon-text-size:before {
  content: "\e241";
}
.glyphicon-text-color:before {
  content: "\e242";
}
.glyphicon-text-background:before {
  content: "\e243";
}
.glyphicon-object-align-top:before {
  content: "\e244";
}
.glyphicon-object-align-bottom:before {
  content: "\e245";
}
.glyphicon-object-align-horizontal:before {
  content: "\e246";
}
.glyphicon-object-align-left:before {
  content: "\e247";
}
.glyphicon-object-align-vertical:before {
  content: "\e248";
}
.glyphicon-object-align-right:before {
  content: "\e249";
}
.glyphicon-triangle-right:before {
  content: "\e250";
}
.glyphicon-triangle-left:before {
  content: "\e251";
}
.glyphicon-triangle-bottom:before {
  content: "\e252";
}
.glyphicon-triangle-top:before {
  content: "\e253";
}
.glyphicon-console:before {
  content: "\e254";
}
.glyphicon-superscript:before {
  content: "\e255";
}
.glyphicon-subscript:before {
  content: "\e256";
}
.glyphicon-menu-left:before {
  content: "\e257";
}
.glyphicon-menu-right:before {
  content: "\e258";
}
.glyphicon-menu-down:before {
  content: "\e259";
}
.glyphicon-menu-up:before {
  content: "\e260";
}
* {
  -webkit-box-sizing: border-box;
  -moz-box-sizing: border-box;
  box-sizing: border-box;
}
*:before,
*:after {
  -webkit-box-sizing: border-box;
  -moz-box-sizing: border-box;
  box-sizing: border-box;
}
html {
  font-size: 10px;
  -webkit-tap-highlight-color: rgba(0, 0, 0, 0);
}
body {
  font-family: "Helvetica Neue", Helvetica, Arial, sans-serif;
  font-size: 13px;
  line-height: 1.42857143;
  color: #000;
  background-color: #fff;
}
input,
button,
select,
textarea {
  font-family: inherit;
  font-size: inherit;
  line-height: inherit;
}
a {
  color: #337ab7;
  text-decoration: none;
}
a:hover,
a:focus {
  color: #23527c;
  text-decoration: underline;
}
a:focus {
  outline: 5px auto -webkit-focus-ring-color;
  outline-offset: -2px;
}
figure {
  margin: 0;
}
img {
  vertical-align: middle;
}
.img-responsive,
.thumbnail > img,
.thumbnail a > img,
.carousel-inner > .item > img,
.carousel-inner > .item > a > img {
  display: block;
  max-width: 100%;
  height: auto;
}
.img-rounded {
  border-radius: 3px;
}
.img-thumbnail {
  padding: 4px;
  line-height: 1.42857143;
  background-color: #fff;
  border: 1px solid #ddd;
  border-radius: 2px;
  -webkit-transition: all 0.2s ease-in-out;
  -o-transition: all 0.2s ease-in-out;
  transition: all 0.2s ease-in-out;
  display: inline-block;
  max-width: 100%;
  height: auto;
}
.img-circle {
  border-radius: 50%;
}
hr {
  margin-top: 18px;
  margin-bottom: 18px;
  border: 0;
  border-top: 1px solid #eeeeee;
}
.sr-only {
  position: absolute;
  width: 1px;
  height: 1px;
  margin: -1px;
  padding: 0;
  overflow: hidden;
  clip: rect(0, 0, 0, 0);
  border: 0;
}
.sr-only-focusable:active,
.sr-only-focusable:focus {
  position: static;
  width: auto;
  height: auto;
  margin: 0;
  overflow: visible;
  clip: auto;
}
[role="button"] {
  cursor: pointer;
}
h1,
h2,
h3,
h4,
h5,
h6,
.h1,
.h2,
.h3,
.h4,
.h5,
.h6 {
  font-family: inherit;
  font-weight: 500;
  line-height: 1.1;
  color: inherit;
}
h1 small,
h2 small,
h3 small,
h4 small,
h5 small,
h6 small,
.h1 small,
.h2 small,
.h3 small,
.h4 small,
.h5 small,
.h6 small,
h1 .small,
h2 .small,
h3 .small,
h4 .small,
h5 .small,
h6 .small,
.h1 .small,
.h2 .small,
.h3 .small,
.h4 .small,
.h5 .small,
.h6 .small {
  font-weight: normal;
  line-height: 1;
  color: #777777;
}
h1,
.h1,
h2,
.h2,
h3,
.h3 {
  margin-top: 18px;
  margin-bottom: 9px;
}
h1 small,
.h1 small,
h2 small,
.h2 small,
h3 small,
.h3 small,
h1 .small,
.h1 .small,
h2 .small,
.h2 .small,
h3 .small,
.h3 .small {
  font-size: 65%;
}
h4,
.h4,
h5,
.h5,
h6,
.h6 {
  margin-top: 9px;
  margin-bottom: 9px;
}
h4 small,
.h4 small,
h5 small,
.h5 small,
h6 small,
.h6 small,
h4 .small,
.h4 .small,
h5 .small,
.h5 .small,
h6 .small,
.h6 .small {
  font-size: 75%;
}
h1,
.h1 {
  font-size: 33px;
}
h2,
.h2 {
  font-size: 27px;
}
h3,
.h3 {
  font-size: 23px;
}
h4,
.h4 {
  font-size: 17px;
}
h5,
.h5 {
  font-size: 13px;
}
h6,
.h6 {
  font-size: 12px;
}
p {
  margin: 0 0 9px;
}
.lead {
  margin-bottom: 18px;
  font-size: 14px;
  font-weight: 300;
  line-height: 1.4;
}
@media (min-width: 768px) {
  .lead {
    font-size: 19.5px;
  }
}
small,
.small {
  font-size: 92%;
}
mark,
.mark {
  background-color: #fcf8e3;
  padding: .2em;
}
.text-left {
  text-align: left;
}
.text-right {
  text-align: right;
}
.text-center {
  text-align: center;
}
.text-justify {
  text-align: justify;
}
.text-nowrap {
  white-space: nowrap;
}
.text-lowercase {
  text-transform: lowercase;
}
.text-uppercase {
  text-transform: uppercase;
}
.text-capitalize {
  text-transform: capitalize;
}
.text-muted {
  color: #777777;
}
.text-primary {
  color: #337ab7;
}
a.text-primary:hover,
a.text-primary:focus {
  color: #286090;
}
.text-success {
  color: #3c763d;
}
a.text-success:hover,
a.text-success:focus {
  color: #2b542c;
}
.text-info {
  color: #31708f;
}
a.text-info:hover,
a.text-info:focus {
  color: #245269;
}
.text-warning {
  color: #8a6d3b;
}
a.text-warning:hover,
a.text-warning:focus {
  color: #66512c;
}
.text-danger {
  color: #a94442;
}
a.text-danger:hover,
a.text-danger:focus {
  color: #843534;
}
.bg-primary {
  color: #fff;
  background-color: #337ab7;
}
a.bg-primary:hover,
a.bg-primary:focus {
  background-color: #286090;
}
.bg-success {
  background-color: #dff0d8;
}
a.bg-success:hover,
a.bg-success:focus {
  background-color: #c1e2b3;
}
.bg-info {
  background-color: #d9edf7;
}
a.bg-info:hover,
a.bg-info:focus {
  background-color: #afd9ee;
}
.bg-warning {
  background-color: #fcf8e3;
}
a.bg-warning:hover,
a.bg-warning:focus {
  background-color: #f7ecb5;
}
.bg-danger {
  background-color: #f2dede;
}
a.bg-danger:hover,
a.bg-danger:focus {
  background-color: #e4b9b9;
}
.page-header {
  padding-bottom: 8px;
  margin: 36px 0 18px;
  border-bottom: 1px solid #eeeeee;
}
ul,
ol {
  margin-top: 0;
  margin-bottom: 9px;
}
ul ul,
ol ul,
ul ol,
ol ol {
  margin-bottom: 0;
}
.list-unstyled {
  padding-left: 0;
  list-style: none;
}
.list-inline {
  padding-left: 0;
  list-style: none;
  margin-left: -5px;
}
.list-inline > li {
  display: inline-block;
  padding-left: 5px;
  padding-right: 5px;
}
dl {
  margin-top: 0;
  margin-bottom: 18px;
}
dt,
dd {
  line-height: 1.42857143;
}
dt {
  font-weight: bold;
}
dd {
  margin-left: 0;
}
@media (min-width: 541px) {
  .dl-horizontal dt {
    float: left;
    width: 160px;
    clear: left;
    text-align: right;
    overflow: hidden;
    text-overflow: ellipsis;
    white-space: nowrap;
  }
  .dl-horizontal dd {
    margin-left: 180px;
  }
}
abbr[title],
abbr[data-original-title] {
  cursor: help;
  border-bottom: 1px dotted #777777;
}
.initialism {
  font-size: 90%;
  text-transform: uppercase;
}
blockquote {
  padding: 9px 18px;
  margin: 0 0 18px;
  font-size: inherit;
  border-left: 5px solid #eeeeee;
}
blockquote p:last-child,
blockquote ul:last-child,
blockquote ol:last-child {
  margin-bottom: 0;
}
blockquote footer,
blockquote small,
blockquote .small {
  display: block;
  font-size: 80%;
  line-height: 1.42857143;
  color: #777777;
}
blockquote footer:before,
blockquote small:before,
blockquote .small:before {
  content: '\2014 \00A0';
}
.blockquote-reverse,
blockquote.pull-right {
  padding-right: 15px;
  padding-left: 0;
  border-right: 5px solid #eeeeee;
  border-left: 0;
  text-align: right;
}
.blockquote-reverse footer:before,
blockquote.pull-right footer:before,
.blockquote-reverse small:before,
blockquote.pull-right small:before,
.blockquote-reverse .small:before,
blockquote.pull-right .small:before {
  content: '';
}
.blockquote-reverse footer:after,
blockquote.pull-right footer:after,
.blockquote-reverse small:after,
blockquote.pull-right small:after,
.blockquote-reverse .small:after,
blockquote.pull-right .small:after {
  content: '\00A0 \2014';
}
address {
  margin-bottom: 18px;
  font-style: normal;
  line-height: 1.42857143;
}
code,
kbd,
pre,
samp {
  font-family: monospace;
}
code {
  padding: 2px 4px;
  font-size: 90%;
  color: #c7254e;
  background-color: #f9f2f4;
  border-radius: 2px;
}
kbd {
  padding: 2px 4px;
  font-size: 90%;
  color: #888;
  background-color: transparent;
  border-radius: 1px;
  box-shadow: inset 0 -1px 0 rgba(0, 0, 0, 0.25);
}
kbd kbd {
  padding: 0;
  font-size: 100%;
  font-weight: bold;
  box-shadow: none;
}
pre {
  display: block;
  padding: 8.5px;
  margin: 0 0 9px;
  font-size: 12px;
  line-height: 1.42857143;
  word-break: break-all;
  word-wrap: break-word;
  color: #333333;
  background-color: #f5f5f5;
  border: 1px solid #ccc;
  border-radius: 2px;
}
pre code {
  padding: 0;
  font-size: inherit;
  color: inherit;
  white-space: pre-wrap;
  background-color: transparent;
  border-radius: 0;
}
.pre-scrollable {
  max-height: 340px;
  overflow-y: scroll;
}
.container {
  margin-right: auto;
  margin-left: auto;
  padding-left: 0px;
  padding-right: 0px;
}
@media (min-width: 768px) {
  .container {
    width: 768px;
  }
}
@media (min-width: 992px) {
  .container {
    width: 940px;
  }
}
@media (min-width: 1200px) {
  .container {
    width: 1140px;
  }
}
.container-fluid {
  margin-right: auto;
  margin-left: auto;
  padding-left: 0px;
  padding-right: 0px;
}
.row {
  margin-left: 0px;
  margin-right: 0px;
}
.col-xs-1, .col-sm-1, .col-md-1, .col-lg-1, .col-xs-2, .col-sm-2, .col-md-2, .col-lg-2, .col-xs-3, .col-sm-3, .col-md-3, .col-lg-3, .col-xs-4, .col-sm-4, .col-md-4, .col-lg-4, .col-xs-5, .col-sm-5, .col-md-5, .col-lg-5, .col-xs-6, .col-sm-6, .col-md-6, .col-lg-6, .col-xs-7, .col-sm-7, .col-md-7, .col-lg-7, .col-xs-8, .col-sm-8, .col-md-8, .col-lg-8, .col-xs-9, .col-sm-9, .col-md-9, .col-lg-9, .col-xs-10, .col-sm-10, .col-md-10, .col-lg-10, .col-xs-11, .col-sm-11, .col-md-11, .col-lg-11, .col-xs-12, .col-sm-12, .col-md-12, .col-lg-12 {
  position: relative;
  min-height: 1px;
  padding-left: 0px;
  padding-right: 0px;
}
.col-xs-1, .col-xs-2, .col-xs-3, .col-xs-4, .col-xs-5, .col-xs-6, .col-xs-7, .col-xs-8, .col-xs-9, .col-xs-10, .col-xs-11, .col-xs-12 {
  float: left;
}
.col-xs-12 {
  width: 100%;
}
.col-xs-11 {
  width: 91.66666667%;
}
.col-xs-10 {
  width: 83.33333333%;
}
.col-xs-9 {
  width: 75%;
}
.col-xs-8 {
  width: 66.66666667%;
}
.col-xs-7 {
  width: 58.33333333%;
}
.col-xs-6 {
  width: 50%;
}
.col-xs-5 {
  width: 41.66666667%;
}
.col-xs-4 {
  width: 33.33333333%;
}
.col-xs-3 {
  width: 25%;
}
.col-xs-2 {
  width: 16.66666667%;
}
.col-xs-1 {
  width: 8.33333333%;
}
.col-xs-pull-12 {
  right: 100%;
}
.col-xs-pull-11 {
  right: 91.66666667%;
}
.col-xs-pull-10 {
  right: 83.33333333%;
}
.col-xs-pull-9 {
  right: 75%;
}
.col-xs-pull-8 {
  right: 66.66666667%;
}
.col-xs-pull-7 {
  right: 58.33333333%;
}
.col-xs-pull-6 {
  right: 50%;
}
.col-xs-pull-5 {
  right: 41.66666667%;
}
.col-xs-pull-4 {
  right: 33.33333333%;
}
.col-xs-pull-3 {
  right: 25%;
}
.col-xs-pull-2 {
  right: 16.66666667%;
}
.col-xs-pull-1 {
  right: 8.33333333%;
}
.col-xs-pull-0 {
  right: auto;
}
.col-xs-push-12 {
  left: 100%;
}
.col-xs-push-11 {
  left: 91.66666667%;
}
.col-xs-push-10 {
  left: 83.33333333%;
}
.col-xs-push-9 {
  left: 75%;
}
.col-xs-push-8 {
  left: 66.66666667%;
}
.col-xs-push-7 {
  left: 58.33333333%;
}
.col-xs-push-6 {
  left: 50%;
}
.col-xs-push-5 {
  left: 41.66666667%;
}
.col-xs-push-4 {
  left: 33.33333333%;
}
.col-xs-push-3 {
  left: 25%;
}
.col-xs-push-2 {
  left: 16.66666667%;
}
.col-xs-push-1 {
  left: 8.33333333%;
}
.col-xs-push-0 {
  left: auto;
}
.col-xs-offset-12 {
  margin-left: 100%;
}
.col-xs-offset-11 {
  margin-left: 91.66666667%;
}
.col-xs-offset-10 {
  margin-left: 83.33333333%;
}
.col-xs-offset-9 {
  margin-left: 75%;
}
.col-xs-offset-8 {
  margin-left: 66.66666667%;
}
.col-xs-offset-7 {
  margin-left: 58.33333333%;
}
.col-xs-offset-6 {
  margin-left: 50%;
}
.col-xs-offset-5 {
  margin-left: 41.66666667%;
}
.col-xs-offset-4 {
  margin-left: 33.33333333%;
}
.col-xs-offset-3 {
  margin-left: 25%;
}
.col-xs-offset-2 {
  margin-left: 16.66666667%;
}
.col-xs-offset-1 {
  margin-left: 8.33333333%;
}
.col-xs-offset-0 {
  margin-left: 0%;
}
@media (min-width: 768px) {
  .col-sm-1, .col-sm-2, .col-sm-3, .col-sm-4, .col-sm-5, .col-sm-6, .col-sm-7, .col-sm-8, .col-sm-9, .col-sm-10, .col-sm-11, .col-sm-12 {
    float: left;
  }
  .col-sm-12 {
    width: 100%;
  }
  .col-sm-11 {
    width: 91.66666667%;
  }
  .col-sm-10 {
    width: 83.33333333%;
  }
  .col-sm-9 {
    width: 75%;
  }
  .col-sm-8 {
    width: 66.66666667%;
  }
  .col-sm-7 {
    width: 58.33333333%;
  }
  .col-sm-6 {
    width: 50%;
  }
  .col-sm-5 {
    width: 41.66666667%;
  }
  .col-sm-4 {
    width: 33.33333333%;
  }
  .col-sm-3 {
    width: 25%;
  }
  .col-sm-2 {
    width: 16.66666667%;
  }
  .col-sm-1 {
    width: 8.33333333%;
  }
  .col-sm-pull-12 {
    right: 100%;
  }
  .col-sm-pull-11 {
    right: 91.66666667%;
  }
  .col-sm-pull-10 {
    right: 83.33333333%;
  }
  .col-sm-pull-9 {
    right: 75%;
  }
  .col-sm-pull-8 {
    right: 66.66666667%;
  }
  .col-sm-pull-7 {
    right: 58.33333333%;
  }
  .col-sm-pull-6 {
    right: 50%;
  }
  .col-sm-pull-5 {
    right: 41.66666667%;
  }
  .col-sm-pull-4 {
    right: 33.33333333%;
  }
  .col-sm-pull-3 {
    right: 25%;
  }
  .col-sm-pull-2 {
    right: 16.66666667%;
  }
  .col-sm-pull-1 {
    right: 8.33333333%;
  }
  .col-sm-pull-0 {
    right: auto;
  }
  .col-sm-push-12 {
    left: 100%;
  }
  .col-sm-push-11 {
    left: 91.66666667%;
  }
  .col-sm-push-10 {
    left: 83.33333333%;
  }
  .col-sm-push-9 {
    left: 75%;
  }
  .col-sm-push-8 {
    left: 66.66666667%;
  }
  .col-sm-push-7 {
    left: 58.33333333%;
  }
  .col-sm-push-6 {
    left: 50%;
  }
  .col-sm-push-5 {
    left: 41.66666667%;
  }
  .col-sm-push-4 {
    left: 33.33333333%;
  }
  .col-sm-push-3 {
    left: 25%;
  }
  .col-sm-push-2 {
    left: 16.66666667%;
  }
  .col-sm-push-1 {
    left: 8.33333333%;
  }
  .col-sm-push-0 {
    left: auto;
  }
  .col-sm-offset-12 {
    margin-left: 100%;
  }
  .col-sm-offset-11 {
    margin-left: 91.66666667%;
  }
  .col-sm-offset-10 {
    margin-left: 83.33333333%;
  }
  .col-sm-offset-9 {
    margin-left: 75%;
  }
  .col-sm-offset-8 {
    margin-left: 66.66666667%;
  }
  .col-sm-offset-7 {
    margin-left: 58.33333333%;
  }
  .col-sm-offset-6 {
    margin-left: 50%;
  }
  .col-sm-offset-5 {
    margin-left: 41.66666667%;
  }
  .col-sm-offset-4 {
    margin-left: 33.33333333%;
  }
  .col-sm-offset-3 {
    margin-left: 25%;
  }
  .col-sm-offset-2 {
    margin-left: 16.66666667%;
  }
  .col-sm-offset-1 {
    margin-left: 8.33333333%;
  }
  .col-sm-offset-0 {
    margin-left: 0%;
  }
}
@media (min-width: 992px) {
  .col-md-1, .col-md-2, .col-md-3, .col-md-4, .col-md-5, .col-md-6, .col-md-7, .col-md-8, .col-md-9, .col-md-10, .col-md-11, .col-md-12 {
    float: left;
  }
  .col-md-12 {
    width: 100%;
  }
  .col-md-11 {
    width: 91.66666667%;
  }
  .col-md-10 {
    width: 83.33333333%;
  }
  .col-md-9 {
    width: 75%;
  }
  .col-md-8 {
    width: 66.66666667%;
  }
  .col-md-7 {
    width: 58.33333333%;
  }
  .col-md-6 {
    width: 50%;
  }
  .col-md-5 {
    width: 41.66666667%;
  }
  .col-md-4 {
    width: 33.33333333%;
  }
  .col-md-3 {
    width: 25%;
  }
  .col-md-2 {
    width: 16.66666667%;
  }
  .col-md-1 {
    width: 8.33333333%;
  }
  .col-md-pull-12 {
    right: 100%;
  }
  .col-md-pull-11 {
    right: 91.66666667%;
  }
  .col-md-pull-10 {
    right: 83.33333333%;
  }
  .col-md-pull-9 {
    right: 75%;
  }
  .col-md-pull-8 {
    right: 66.66666667%;
  }
  .col-md-pull-7 {
    right: 58.33333333%;
  }
  .col-md-pull-6 {
    right: 50%;
  }
  .col-md-pull-5 {
    right: 41.66666667%;
  }
  .col-md-pull-4 {
    right: 33.33333333%;
  }
  .col-md-pull-3 {
    right: 25%;
  }
  .col-md-pull-2 {
    right: 16.66666667%;
  }
  .col-md-pull-1 {
    right: 8.33333333%;
  }
  .col-md-pull-0 {
    right: auto;
  }
  .col-md-push-12 {
    left: 100%;
  }
  .col-md-push-11 {
    left: 91.66666667%;
  }
  .col-md-push-10 {
    left: 83.33333333%;
  }
  .col-md-push-9 {
    left: 75%;
  }
  .col-md-push-8 {
    left: 66.66666667%;
  }
  .col-md-push-7 {
    left: 58.33333333%;
  }
  .col-md-push-6 {
    left: 50%;
  }
  .col-md-push-5 {
    left: 41.66666667%;
  }
  .col-md-push-4 {
    left: 33.33333333%;
  }
  .col-md-push-3 {
    left: 25%;
  }
  .col-md-push-2 {
    left: 16.66666667%;
  }
  .col-md-push-1 {
    left: 8.33333333%;
  }
  .col-md-push-0 {
    left: auto;
  }
  .col-md-offset-12 {
    margin-left: 100%;
  }
  .col-md-offset-11 {
    margin-left: 91.66666667%;
  }
  .col-md-offset-10 {
    margin-left: 83.33333333%;
  }
  .col-md-offset-9 {
    margin-left: 75%;
  }
  .col-md-offset-8 {
    margin-left: 66.66666667%;
  }
  .col-md-offset-7 {
    margin-left: 58.33333333%;
  }
  .col-md-offset-6 {
    margin-left: 50%;
  }
  .col-md-offset-5 {
    margin-left: 41.66666667%;
  }
  .col-md-offset-4 {
    margin-left: 33.33333333%;
  }
  .col-md-offset-3 {
    margin-left: 25%;
  }
  .col-md-offset-2 {
    margin-left: 16.66666667%;
  }
  .col-md-offset-1 {
    margin-left: 8.33333333%;
  }
  .col-md-offset-0 {
    margin-left: 0%;
  }
}
@media (min-width: 1200px) {
  .col-lg-1, .col-lg-2, .col-lg-3, .col-lg-4, .col-lg-5, .col-lg-6, .col-lg-7, .col-lg-8, .col-lg-9, .col-lg-10, .col-lg-11, .col-lg-12 {
    float: left;
  }
  .col-lg-12 {
    width: 100%;
  }
  .col-lg-11 {
    width: 91.66666667%;
  }
  .col-lg-10 {
    width: 83.33333333%;
  }
  .col-lg-9 {
    width: 75%;
  }
  .col-lg-8 {
    width: 66.66666667%;
  }
  .col-lg-7 {
    width: 58.33333333%;
  }
  .col-lg-6 {
    width: 50%;
  }
  .col-lg-5 {
    width: 41.66666667%;
  }
  .col-lg-4 {
    width: 33.33333333%;
  }
  .col-lg-3 {
    width: 25%;
  }
  .col-lg-2 {
    width: 16.66666667%;
  }
  .col-lg-1 {
    width: 8.33333333%;
  }
  .col-lg-pull-12 {
    right: 100%;
  }
  .col-lg-pull-11 {
    right: 91.66666667%;
  }
  .col-lg-pull-10 {
    right: 83.33333333%;
  }
  .col-lg-pull-9 {
    right: 75%;
  }
  .col-lg-pull-8 {
    right: 66.66666667%;
  }
  .col-lg-pull-7 {
    right: 58.33333333%;
  }
  .col-lg-pull-6 {
    right: 50%;
  }
  .col-lg-pull-5 {
    right: 41.66666667%;
  }
  .col-lg-pull-4 {
    right: 33.33333333%;
  }
  .col-lg-pull-3 {
    right: 25%;
  }
  .col-lg-pull-2 {
    right: 16.66666667%;
  }
  .col-lg-pull-1 {
    right: 8.33333333%;
  }
  .col-lg-pull-0 {
    right: auto;
  }
  .col-lg-push-12 {
    left: 100%;
  }
  .col-lg-push-11 {
    left: 91.66666667%;
  }
  .col-lg-push-10 {
    left: 83.33333333%;
  }
  .col-lg-push-9 {
    left: 75%;
  }
  .col-lg-push-8 {
    left: 66.66666667%;
  }
  .col-lg-push-7 {
    left: 58.33333333%;
  }
  .col-lg-push-6 {
    left: 50%;
  }
  .col-lg-push-5 {
    left: 41.66666667%;
  }
  .col-lg-push-4 {
    left: 33.33333333%;
  }
  .col-lg-push-3 {
    left: 25%;
  }
  .col-lg-push-2 {
    left: 16.66666667%;
  }
  .col-lg-push-1 {
    left: 8.33333333%;
  }
  .col-lg-push-0 {
    left: auto;
  }
  .col-lg-offset-12 {
    margin-left: 100%;
  }
  .col-lg-offset-11 {
    margin-left: 91.66666667%;
  }
  .col-lg-offset-10 {
    margin-left: 83.33333333%;
  }
  .col-lg-offset-9 {
    margin-left: 75%;
  }
  .col-lg-offset-8 {
    margin-left: 66.66666667%;
  }
  .col-lg-offset-7 {
    margin-left: 58.33333333%;
  }
  .col-lg-offset-6 {
    margin-left: 50%;
  }
  .col-lg-offset-5 {
    margin-left: 41.66666667%;
  }
  .col-lg-offset-4 {
    margin-left: 33.33333333%;
  }
  .col-lg-offset-3 {
    margin-left: 25%;
  }
  .col-lg-offset-2 {
    margin-left: 16.66666667%;
  }
  .col-lg-offset-1 {
    margin-left: 8.33333333%;
  }
  .col-lg-offset-0 {
    margin-left: 0%;
  }
}
table {
  background-color: transparent;
}
caption {
  padding-top: 8px;
  padding-bottom: 8px;
  color: #777777;
  text-align: left;
}
th {
  text-align: left;
}
.table {
  width: 100%;
  max-width: 100%;
  margin-bottom: 18px;
}
.table > thead > tr > th,
.table > tbody > tr > th,
.table > tfoot > tr > th,
.table > thead > tr > td,
.table > tbody > tr > td,
.table > tfoot > tr > td {
  padding: 8px;
  line-height: 1.42857143;
  vertical-align: top;
  border-top: 1px solid #ddd;
}
.table > thead > tr > th {
  vertical-align: bottom;
  border-bottom: 2px solid #ddd;
}
.table > caption + thead > tr:first-child > th,
.table > colgroup + thead > tr:first-child > th,
.table > thead:first-child > tr:first-child > th,
.table > caption + thead > tr:first-child > td,
.table > colgroup + thead > tr:first-child > td,
.table > thead:first-child > tr:first-child > td {
  border-top: 0;
}
.table > tbody + tbody {
  border-top: 2px solid #ddd;
}
.table .table {
  background-color: #fff;
}
.table-condensed > thead > tr > th,
.table-condensed > tbody > tr > th,
.table-condensed > tfoot > tr > th,
.table-condensed > thead > tr > td,
.table-condensed > tbody > tr > td,
.table-condensed > tfoot > tr > td {
  padding: 5px;
}
.table-bordered {
  border: 1px solid #ddd;
}
.table-bordered > thead > tr > th,
.table-bordered > tbody > tr > th,
.table-bordered > tfoot > tr > th,
.table-bordered > thead > tr > td,
.table-bordered > tbody > tr > td,
.table-bordered > tfoot > tr > td {
  border: 1px solid #ddd;
}
.table-bordered > thead > tr > th,
.table-bordered > thead > tr > td {
  border-bottom-width: 2px;
}
.table-striped > tbody > tr:nth-of-type(odd) {
  background-color: #f9f9f9;
}
.table-hover > tbody > tr:hover {
  background-color: #f5f5f5;
}
table col[class*="col-"] {
  position: static;
  float: none;
  display: table-column;
}
table td[class*="col-"],
table th[class*="col-"] {
  position: static;
  float: none;
  display: table-cell;
}
.table > thead > tr > td.active,
.table > tbody > tr > td.active,
.table > tfoot > tr > td.active,
.table > thead > tr > th.active,
.table > tbody > tr > th.active,
.table > tfoot > tr > th.active,
.table > thead > tr.active > td,
.table > tbody > tr.active > td,
.table > tfoot > tr.active > td,
.table > thead > tr.active > th,
.table > tbody > tr.active > th,
.table > tfoot > tr.active > th {
  background-color: #f5f5f5;
}
.table-hover > tbody > tr > td.active:hover,
.table-hover > tbody > tr > th.active:hover,
.table-hover > tbody > tr.active:hover > td,
.table-hover > tbody > tr:hover > .active,
.table-hover > tbody > tr.active:hover > th {
  background-color: #e8e8e8;
}
.table > thead > tr > td.success,
.table > tbody > tr > td.success,
.table > tfoot > tr > td.success,
.table > thead > tr > th.success,
.table > tbody > tr > th.success,
.table > tfoot > tr > th.success,
.table > thead > tr.success > td,
.table > tbody > tr.success > td,
.table > tfoot > tr.success > td,
.table > thead > tr.success > th,
.table > tbody > tr.success > th,
.table > tfoot > tr.success > th {
  background-color: #dff0d8;
}
.table-hover > tbody > tr > td.success:hover,
.table-hover > tbody > tr > th.success:hover,
.table-hover > tbody > tr.success:hover > td,
.table-hover > tbody > tr:hover > .success,
.table-hover > tbody > tr.success:hover > th {
  background-color: #d0e9c6;
}
.table > thead > tr > td.info,
.table > tbody > tr > td.info,
.table > tfoot > tr > td.info,
.table > thead > tr > th.info,
.table > tbody > tr > th.info,
.table > tfoot > tr > th.info,
.table > thead > tr.info > td,
.table > tbody > tr.info > td,
.table > tfoot > tr.info > td,
.table > thead > tr.info > th,
.table > tbody > tr.info > th,
.table > tfoot > tr.info > th {
  background-color: #d9edf7;
}
.table-hover > tbody > tr > td.info:hover,
.table-hover > tbody > tr > th.info:hover,
.table-hover > tbody > tr.info:hover > td,
.table-hover > tbody > tr:hover > .info,
.table-hover > tbody > tr.info:hover > th {
  background-color: #c4e3f3;
}
.table > thead > tr > td.warning,
.table > tbody > tr > td.warning,
.table > tfoot > tr > td.warning,
.table > thead > tr > th.warning,
.table > tbody > tr > th.warning,
.table > tfoot > tr > th.warning,
.table > thead > tr.warning > td,
.table > tbody > tr.warning > td,
.table > tfoot > tr.warning > td,
.table > thead > tr.warning > th,
.table > tbody > tr.warning > th,
.table > tfoot > tr.warning > th {
  background-color: #fcf8e3;
}
.table-hover > tbody > tr > td.warning:hover,
.table-hover > tbody > tr > th.warning:hover,
.table-hover > tbody > tr.warning:hover > td,
.table-hover > tbody > tr:hover > .warning,
.table-hover > tbody > tr.warning:hover > th {
  background-color: #faf2cc;
}
.table > thead > tr > td.danger,
.table > tbody > tr > td.danger,
.table > tfoot > tr > td.danger,
.table > thead > tr > th.danger,
.table > tbody > tr > th.danger,
.table > tfoot > tr > th.danger,
.table > thead > tr.danger > td,
.table > tbody > tr.danger > td,
.table > tfoot > tr.danger > td,
.table > thead > tr.danger > th,
.table > tbody > tr.danger > th,
.table > tfoot > tr.danger > th {
  background-color: #f2dede;
}
.table-hover > tbody > tr > td.danger:hover,
.table-hover > tbody > tr > th.danger:hover,
.table-hover > tbody > tr.danger:hover > td,
.table-hover > tbody > tr:hover > .danger,
.table-hover > tbody > tr.danger:hover > th {
  background-color: #ebcccc;
}
.table-responsive {
  overflow-x: auto;
  min-height: 0.01%;
}
@media screen and (max-width: 767px) {
  .table-responsive {
    width: 100%;
    margin-bottom: 13.5px;
    overflow-y: hidden;
    -ms-overflow-style: -ms-autohiding-scrollbar;
    border: 1px solid #ddd;
  }
  .table-responsive > .table {
    margin-bottom: 0;
  }
  .table-responsive > .table > thead > tr > th,
  .table-responsive > .table > tbody > tr > th,
  .table-responsive > .table > tfoot > tr > th,
  .table-responsive > .table > thead > tr > td,
  .table-responsive > .table > tbody > tr > td,
  .table-responsive > .table > tfoot > tr > td {
    white-space: nowrap;
  }
  .table-responsive > .table-bordered {
    border: 0;
  }
  .table-responsive > .table-bordered > thead > tr > th:first-child,
  .table-responsive > .table-bordered > tbody > tr > th:first-child,
  .table-responsive > .table-bordered > tfoot > tr > th:first-child,
  .table-responsive > .table-bordered > thead > tr > td:first-child,
  .table-responsive > .table-bordered > tbody > tr > td:first-child,
  .table-responsive > .table-bordered > tfoot > tr > td:first-child {
    border-left: 0;
  }
  .table-responsive > .table-bordered > thead > tr > th:last-child,
  .table-responsive > .table-bordered > tbody > tr > th:last-child,
  .table-responsive > .table-bordered > tfoot > tr > th:last-child,
  .table-responsive > .table-bordered > thead > tr > td:last-child,
  .table-responsive > .table-bordered > tbody > tr > td:last-child,
  .table-responsive > .table-bordered > tfoot > tr > td:last-child {
    border-right: 0;
  }
  .table-responsive > .table-bordered > tbody > tr:last-child > th,
  .table-responsive > .table-bordered > tfoot > tr:last-child > th,
  .table-responsive > .table-bordered > tbody > tr:last-child > td,
  .table-responsive > .table-bordered > tfoot > tr:last-child > td {
    border-bottom: 0;
  }
}
fieldset {
  padding: 0;
  margin: 0;
  border: 0;
  min-width: 0;
}
legend {
  display: block;
  width: 100%;
  padding: 0;
  margin-bottom: 18px;
  font-size: 19.5px;
  line-height: inherit;
  color: #333333;
  border: 0;
  border-bottom: 1px solid #e5e5e5;
}
label {
  display: inline-block;
  max-width: 100%;
  margin-bottom: 5px;
  font-weight: bold;
}
input[type="search"] {
  -webkit-box-sizing: border-box;
  -moz-box-sizing: border-box;
  box-sizing: border-box;
}
input[type="radio"],
input[type="checkbox"] {
  margin: 4px 0 0;
  margin-top: 1px \9;
  line-height: normal;
}
input[type="file"] {
  display: block;
}
input[type="range"] {
  display: block;
  width: 100%;
}
select[multiple],
select[size] {
  height: auto;
}
input[type="file"]:focus,
input[type="radio"]:focus,
input[type="checkbox"]:focus {
  outline: 5px auto -webkit-focus-ring-color;
  outline-offset: -2px;
}
output {
  display: block;
  padding-top: 7px;
  font-size: 13px;
  line-height: 1.42857143;
  color: #555555;
}
.form-control {
  display: block;
  width: 100%;
  height: 32px;
  padding: 6px 12px;
  font-size: 13px;
  line-height: 1.42857143;
  color: #555555;
  background-color: #fff;
  background-image: none;
  border: 1px solid #ccc;
  border-radius: 2px;
  -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075);
  box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075);
  -webkit-transition: border-color ease-in-out .15s, box-shadow ease-in-out .15s;
  -o-transition: border-color ease-in-out .15s, box-shadow ease-in-out .15s;
  transition: border-color ease-in-out .15s, box-shadow ease-in-out .15s;
}
.form-control:focus {
  border-color: #66afe9;
  outline: 0;
  -webkit-box-shadow: inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6);
  box-shadow: inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6);
}
.form-control::-moz-placeholder {
  color: #999;
  opacity: 1;
}
.form-control:-ms-input-placeholder {
  color: #999;
}
.form-control::-webkit-input-placeholder {
  color: #999;
}
.form-control::-ms-expand {
  border: 0;
  background-color: transparent;
}
.form-control[disabled],
.form-control[readonly],
fieldset[disabled] .form-control {
  background-color: #eeeeee;
  opacity: 1;
}
.form-control[disabled],
fieldset[disabled] .form-control {
  cursor: not-allowed;
}
textarea.form-control {
  height: auto;
}
input[type="search"] {
  -webkit-appearance: none;
}
@media screen and (-webkit-min-device-pixel-ratio: 0) {
  input[type="date"].form-control,
  input[type="time"].form-control,
  input[type="datetime-local"].form-control,
  input[type="month"].form-control {
    line-height: 32px;
  }
  input[type="date"].input-sm,
  input[type="time"].input-sm,
  input[type="datetime-local"].input-sm,
  input[type="month"].input-sm,
  .input-group-sm input[type="date"],
  .input-group-sm input[type="time"],
  .input-group-sm input[type="datetime-local"],
  .input-group-sm input[type="month"] {
    line-height: 30px;
  }
  input[type="date"].input-lg,
  input[type="time"].input-lg,
  input[type="datetime-local"].input-lg,
  input[type="month"].input-lg,
  .input-group-lg input[type="date"],
  .input-group-lg input[type="time"],
  .input-group-lg input[type="datetime-local"],
  .input-group-lg input[type="month"] {
    line-height: 45px;
  }
}
.form-group {
  margin-bottom: 15px;
}
.radio,
.checkbox {
  position: relative;
  display: block;
  margin-top: 10px;
  margin-bottom: 10px;
}
.radio label,
.checkbox label {
  min-height: 18px;
  padding-left: 20px;
  margin-bottom: 0;
  font-weight: normal;
  cursor: pointer;
}
.radio input[type="radio"],
.radio-inline input[type="radio"],
.checkbox input[type="checkbox"],
.checkbox-inline input[type="checkbox"] {
  position: absolute;
  margin-left: -20px;
  margin-top: 4px \9;
}
.radio + .radio,
.checkbox + .checkbox {
  margin-top: -5px;
}
.radio-inline,
.checkbox-inline {
  position: relative;
  display: inline-block;
  padding-left: 20px;
  margin-bottom: 0;
  vertical-align: middle;
  font-weight: normal;
  cursor: pointer;
}
.radio-inline + .radio-inline,
.checkbox-inline + .checkbox-inline {
  margin-top: 0;
  margin-left: 10px;
}
input[type="radio"][disabled],
input[type="checkbox"][disabled],
input[type="radio"].disabled,
input[type="checkbox"].disabled,
fieldset[disabled] input[type="radio"],
fieldset[disabled] input[type="checkbox"] {
  cursor: not-allowed;
}
.radio-inline.disabled,
.checkbox-inline.disabled,
fieldset[disabled] .radio-inline,
fieldset[disabled] .checkbox-inline {
  cursor: not-allowed;
}
.radio.disabled label,
.checkbox.disabled label,
fieldset[disabled] .radio label,
fieldset[disabled] .checkbox label {
  cursor: not-allowed;
}
.form-control-static {
  padding-top: 7px;
  padding-bottom: 7px;
  margin-bottom: 0;
  min-height: 31px;
}
.form-control-static.input-lg,
.form-control-static.input-sm {
  padding-left: 0;
  padding-right: 0;
}
.input-sm {
  height: 30px;
  padding: 5px 10px;
  font-size: 12px;
  line-height: 1.5;
  border-radius: 1px;
}
select.input-sm {
  height: 30px;
  line-height: 30px;
}
textarea.input-sm,
select[multiple].input-sm {
  height: auto;
}
.form-group-sm .form-control {
  height: 30px;
  padding: 5px 10px;
  font-size: 12px;
  line-height: 1.5;
  border-radius: 1px;
}
.form-group-sm select.form-control {
  height: 30px;
  line-height: 30px;
}
.form-group-sm textarea.form-control,
.form-group-sm select[multiple].form-control {
  height: auto;
}
.form-group-sm .form-control-static {
  height: 30px;
  min-height: 30px;
  padding: 6px 10px;
  font-size: 12px;
  line-height: 1.5;
}
.input-lg {
  height: 45px;
  padding: 10px 16px;
  font-size: 17px;
  line-height: 1.3333333;
  border-radius: 3px;
}
select.input-lg {
  height: 45px;
  line-height: 45px;
}
textarea.input-lg,
select[multiple].input-lg {
  height: auto;
}
.form-group-lg .form-control {
  height: 45px;
  padding: 10px 16px;
  font-size: 17px;
  line-height: 1.3333333;
  border-radius: 3px;
}
.form-group-lg select.form-control {
  height: 45px;
  line-height: 45px;
}
.form-group-lg textarea.form-control,
.form-group-lg select[multiple].form-control {
  height: auto;
}
.form-group-lg .form-control-static {
  height: 45px;
  min-height: 35px;
  padding: 11px 16px;
  font-size: 17px;
  line-height: 1.3333333;
}
.has-feedback {
  position: relative;
}
.has-feedback .form-control {
  padding-right: 40px;
}
.form-control-feedback {
  position: absolute;
  top: 0;
  right: 0;
  z-index: 2;
  display: block;
  width: 32px;
  height: 32px;
  line-height: 32px;
  text-align: center;
  pointer-events: none;
}
.input-lg + .form-control-feedback,
.input-group-lg + .form-control-feedback,
.form-group-lg .form-control + .form-control-feedback {
  width: 45px;
  height: 45px;
  line-height: 45px;
}
.input-sm + .form-control-feedback,
.input-group-sm + .form-control-feedback,
.form-group-sm .form-control + .form-control-feedback {
  width: 30px;
  height: 30px;
  line-height: 30px;
}
.has-success .help-block,
.has-success .control-label,
.has-success .radio,
.has-success .checkbox,
.has-success .radio-inline,
.has-success .checkbox-inline,
.has-success.radio label,
.has-success.checkbox label,
.has-success.radio-inline label,
.has-success.checkbox-inline label {
  color: #3c763d;
}
.has-success .form-control {
  border-color: #3c763d;
  -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075);
  box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075);
}
.has-success .form-control:focus {
  border-color: #2b542c;
  -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075), 0 0 6px #67b168;
  box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075), 0 0 6px #67b168;
}
.has-success .input-group-addon {
  color: #3c763d;
  border-color: #3c763d;
  background-color: #dff0d8;
}
.has-success .form-control-feedback {
  color: #3c763d;
}
.has-warning .help-block,
.has-warning .control-label,
.has-warning .radio,
.has-warning .checkbox,
.has-warning .radio-inline,
.has-warning .checkbox-inline,
.has-warning.radio label,
.has-warning.checkbox label,
.has-warning.radio-inline label,
.has-warning.checkbox-inline label {
  color: #8a6d3b;
}
.has-warning .form-control {
  border-color: #8a6d3b;
  -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075);
  box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075);
}
.has-warning .form-control:focus {
  border-color: #66512c;
  -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075), 0 0 6px #c0a16b;
  box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075), 0 0 6px #c0a16b;
}
.has-warning .input-group-addon {
  color: #8a6d3b;
  border-color: #8a6d3b;
  background-color: #fcf8e3;
}
.has-warning .form-control-feedback {
  color: #8a6d3b;
}
.has-error .help-block,
.has-error .control-label,
.has-error .radio,
.has-error .checkbox,
.has-error .radio-inline,
.has-error .checkbox-inline,
.has-error.radio label,
.has-error.checkbox label,
.has-error.radio-inline label,
.has-error.checkbox-inline label {
  color: #a94442;
}
.has-error .form-control {
  border-color: #a94442;
  -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075);
  box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075);
}
.has-error .form-control:focus {
  border-color: #843534;
  -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075), 0 0 6px #ce8483;
  box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075), 0 0 6px #ce8483;
}
.has-error .input-group-addon {
  color: #a94442;
  border-color: #a94442;
  background-color: #f2dede;
}
.has-error .form-control-feedback {
  color: #a94442;
}
.has-feedback label ~ .form-control-feedback {
  top: 23px;
}
.has-feedback label.sr-only ~ .form-control-feedback {
  top: 0;
}
.help-block {
  display: block;
  margin-top: 5px;
  margin-bottom: 10px;
  color: #404040;
}
@media (min-width: 768px) {
  .form-inline .form-group {
    display: inline-block;
    margin-bottom: 0;
    vertical-align: middle;
  }
  .form-inline .form-control {
    display: inline-block;
    width: auto;
    vertical-align: middle;
  }
  .form-inline .form-control-static {
    display: inline-block;
  }
  .form-inline .input-group {
    display: inline-table;
    vertical-align: middle;
  }
  .form-inline .input-group .input-group-addon,
  .form-inline .input-group .input-group-btn,
  .form-inline .input-group .form-control {
    width: auto;
  }
  .form-inline .input-group > .form-control {
    width: 100%;
  }
  .form-inline .control-label {
    margin-bottom: 0;
    vertical-align: middle;
  }
  .form-inline .radio,
  .form-inline .checkbox {
    display: inline-block;
    margin-top: 0;
    margin-bottom: 0;
    vertical-align: middle;
  }
  .form-inline .radio label,
  .form-inline .checkbox label {
    padding-left: 0;
  }
  .form-inline .radio input[type="radio"],
  .form-inline .checkbox input[type="checkbox"] {
    position: relative;
    margin-left: 0;
  }
  .form-inline .has-feedback .form-control-feedback {
    top: 0;
  }
}
.form-horizontal .radio,
.form-horizontal .checkbox,
.form-horizontal .radio-inline,
.form-horizontal .checkbox-inline {
  margin-top: 0;
  margin-bottom: 0;
  padding-top: 7px;
}
.form-horizontal .radio,
.form-horizontal .checkbox {
  min-height: 25px;
}
.form-horizontal .form-group {
  margin-left: 0px;
  margin-right: 0px;
}
@media (min-width: 768px) {
  .form-horizontal .control-label {
    text-align: right;
    margin-bottom: 0;
    padding-top: 7px;
  }
}
.form-horizontal .has-feedback .form-control-feedback {
  right: 0px;
}
@media (min-width: 768px) {
  .form-horizontal .form-group-lg .control-label {
    padding-top: 11px;
    font-size: 17px;
  }
}
@media (min-width: 768px) {
  .form-horizontal .form-group-sm .control-label {
    padding-top: 6px;
    font-size: 12px;
  }
}
.btn {
  display: inline-block;
  margin-bottom: 0;
  font-weight: normal;
  text-align: center;
  vertical-align: middle;
  touch-action: manipulation;
  cursor: pointer;
  background-image: none;
  border: 1px solid transparent;
  white-space: nowrap;
  padding: 6px 12px;
  font-size: 13px;
  line-height: 1.42857143;
  border-radius: 2px;
  -webkit-user-select: none;
  -moz-user-select: none;
  -ms-user-select: none;
  user-select: none;
}
.btn:focus,
.btn:active:focus,
.btn.active:focus,
.btn.focus,
.btn:active.focus,
.btn.active.focus {
  outline: 5px auto -webkit-focus-ring-color;
  outline-offset: -2px;
}
.btn:hover,
.btn:focus,
.btn.focus {
  color: #333;
  text-decoration: none;
}
.btn:active,
.btn.active {
  outline: 0;
  background-image: none;
  -webkit-box-shadow: inset 0 3px 5px rgba(0, 0, 0, 0.125);
  box-shadow: inset 0 3px 5px rgba(0, 0, 0, 0.125);
}
.btn.disabled,
.btn[disabled],
fieldset[disabled] .btn {
  cursor: not-allowed;
  opacity: 0.65;
  filter: alpha(opacity=65);
  -webkit-box-shadow: none;
  box-shadow: none;
}
a.btn.disabled,
fieldset[disabled] a.btn {
  pointer-events: none;
}
.btn-default {
  color: #333;
  background-color: #fff;
  border-color: #ccc;
}
.btn-default:focus,
.btn-default.focus {
  color: #333;
  background-color: #e6e6e6;
  border-color: #8c8c8c;
}
.btn-default:hover {
  color: #333;
  background-color: #e6e6e6;
  border-color: #adadad;
}
.btn-default:active,
.btn-default.active,
.open > .dropdown-toggle.btn-default {
  color: #333;
  background-color: #e6e6e6;
  border-color: #adadad;
}
.btn-default:active:hover,
.btn-default.active:hover,
.open > .dropdown-toggle.btn-default:hover,
.btn-default:active:focus,
.btn-default.active:focus,
.open > .dropdown-toggle.btn-default:focus,
.btn-default:active.focus,
.btn-default.active.focus,
.open > .dropdown-toggle.btn-default.focus {
  color: #333;
  background-color: #d4d4d4;
  border-color: #8c8c8c;
}
.btn-default:active,
.btn-default.active,
.open > .dropdown-toggle.btn-default {
  background-image: none;
}
.btn-default.disabled:hover,
.btn-default[disabled]:hover,
fieldset[disabled] .btn-default:hover,
.btn-default.disabled:focus,
.btn-default[disabled]:focus,
fieldset[disabled] .btn-default:focus,
.btn-default.disabled.focus,
.btn-default[disabled].focus,
fieldset[disabled] .btn-default.focus {
  background-color: #fff;
  border-color: #ccc;
}
.btn-default .badge {
  color: #fff;
  background-color: #333;
}
.btn-primary {
  color: #fff;
  background-color: #337ab7;
  border-color: #2e6da4;
}
.btn-primary:focus,
.btn-primary.focus {
  color: #fff;
  background-color: #286090;
  border-color: #122b40;
}
.btn-primary:hover {
  color: #fff;
  background-color: #286090;
  border-color: #204d74;
}
.btn-primary:active,
.btn-primary.active,
.open > .dropdown-toggle.btn-primary {
  color: #fff;
  background-color: #286090;
  border-color: #204d74;
}
.btn-primary:active:hover,
.btn-primary.active:hover,
.open > .dropdown-toggle.btn-primary:hover,
.btn-primary:active:focus,
.btn-primary.active:focus,
.open > .dropdown-toggle.btn-primary:focus,
.btn-primary:active.focus,
.btn-primary.active.focus,
.open > .dropdown-toggle.btn-primary.focus {
  color: #fff;
  background-color: #204d74;
  border-color: #122b40;
}
.btn-primary:active,
.btn-primary.active,
.open > .dropdown-toggle.btn-primary {
  background-image: none;
}
.btn-primary.disabled:hover,
.btn-primary[disabled]:hover,
fieldset[disabled] .btn-primary:hover,
.btn-primary.disabled:focus,
.btn-primary[disabled]:focus,
fieldset[disabled] .btn-primary:focus,
.btn-primary.disabled.focus,
.btn-primary[disabled].focus,
fieldset[disabled] .btn-primary.focus {
  background-color: #337ab7;
  border-color: #2e6da4;
}
.btn-primary .badge {
  color: #337ab7;
  background-color: #fff;
}
.btn-success {
  color: #fff;
  background-color: #5cb85c;
  border-color: #4cae4c;
}
.btn-success:focus,
.btn-success.focus {
  color: #fff;
  background-color: #449d44;
  border-color: #255625;
}
.btn-success:hover {
  color: #fff;
  background-color: #449d44;
  border-color: #398439;
}
.btn-success:active,
.btn-success.active,
.open > .dropdown-toggle.btn-success {
  color: #fff;
  background-color: #449d44;
  border-color: #398439;
}
.btn-success:active:hover,
.btn-success.active:hover,
.open > .dropdown-toggle.btn-success:hover,
.btn-success:active:focus,
.btn-success.active:focus,
.open > .dropdown-toggle.btn-success:focus,
.btn-success:active.focus,
.btn-success.active.focus,
.open > .dropdown-toggle.btn-success.focus {
  color: #fff;
  background-color: #398439;
  border-color: #255625;
}
.btn-success:active,
.btn-success.active,
.open > .dropdown-toggle.btn-success {
  background-image: none;
}
.btn-success.disabled:hover,
.btn-success[disabled]:hover,
fieldset[disabled] .btn-success:hover,
.btn-success.disabled:focus,
.btn-success[disabled]:focus,
fieldset[disabled] .btn-success:focus,
.btn-success.disabled.focus,
.btn-success[disabled].focus,
fieldset[disabled] .btn-success.focus {
  background-color: #5cb85c;
  border-color: #4cae4c;
}
.btn-success .badge {
  color: #5cb85c;
  background-color: #fff;
}
.btn-info {
  color: #fff;
  background-color: #5bc0de;
  border-color: #46b8da;
}
.btn-info:focus,
.btn-info.focus {
  color: #fff;
  background-color: #31b0d5;
  border-color: #1b6d85;
}
.btn-info:hover {
  color: #fff;
  background-color: #31b0d5;
  border-color: #269abc;
}
.btn-info:active,
.btn-info.active,
.open > .dropdown-toggle.btn-info {
  color: #fff;
  background-color: #31b0d5;
  border-color: #269abc;
}
.btn-info:active:hover,
.btn-info.active:hover,
.open > .dropdown-toggle.btn-info:hover,
.btn-info:active:focus,
.btn-info.active:focus,
.open > .dropdown-toggle.btn-info:focus,
.btn-info:active.focus,
.btn-info.active.focus,
.open > .dropdown-toggle.btn-info.focus {
  color: #fff;
  background-color: #269abc;
  border-color: #1b6d85;
}
.btn-info:active,
.btn-info.active,
.open > .dropdown-toggle.btn-info {
  background-image: none;
}
.btn-info.disabled:hover,
.btn-info[disabled]:hover,
fieldset[disabled] .btn-info:hover,
.btn-info.disabled:focus,
.btn-info[disabled]:focus,
fieldset[disabled] .btn-info:focus,
.btn-info.disabled.focus,
.btn-info[disabled].focus,
fieldset[disabled] .btn-info.focus {
  background-color: #5bc0de;
  border-color: #46b8da;
}
.btn-info .badge {
  color: #5bc0de;
  background-color: #fff;
}
.btn-warning {
  color: #fff;
  background-color: #f0ad4e;
  border-color: #eea236;
}
.btn-warning:focus,
.btn-warning.focus {
  color: #fff;
  background-color: #ec971f;
  border-color: #985f0d;
}
.btn-warning:hover {
  color: #fff;
  background-color: #ec971f;
  border-color: #d58512;
}
.btn-warning:active,
.btn-warning.active,
.open > .dropdown-toggle.btn-warning {
  color: #fff;
  background-color: #ec971f;
  border-color: #d58512;
}
.btn-warning:active:hover,
.btn-warning.active:hover,
.open > .dropdown-toggle.btn-warning:hover,
.btn-warning:active:focus,
.btn-warning.active:focus,
.open > .dropdown-toggle.btn-warning:focus,
.btn-warning:active.focus,
.btn-warning.active.focus,
.open > .dropdown-toggle.btn-warning.focus {
  color: #fff;
  background-color: #d58512;
  border-color: #985f0d;
}
.btn-warning:active,
.btn-warning.active,
.open > .dropdown-toggle.btn-warning {
  background-image: none;
}
.btn-warning.disabled:hover,
.btn-warning[disabled]:hover,
fieldset[disabled] .btn-warning:hover,
.btn-warning.disabled:focus,
.btn-warning[disabled]:focus,
fieldset[disabled] .btn-warning:focus,
.btn-warning.disabled.focus,
.btn-warning[disabled].focus,
fieldset[disabled] .btn-warning.focus {
  background-color: #f0ad4e;
  border-color: #eea236;
}
.btn-warning .badge {
  color: #f0ad4e;
  background-color: #fff;
}
.btn-danger {
  color: #fff;
  background-color: #d9534f;
  border-color: #d43f3a;
}
.btn-danger:focus,
.btn-danger.focus {
  color: #fff;
  background-color: #c9302c;
  border-color: #761c19;
}
.btn-danger:hover {
  color: #fff;
  background-color: #c9302c;
  border-color: #ac2925;
}
.btn-danger:active,
.btn-danger.active,
.open > .dropdown-toggle.btn-danger {
  color: #fff;
  background-color: #c9302c;
  border-color: #ac2925;
}
.btn-danger:active:hover,
.btn-danger.active:hover,
.open > .dropdown-toggle.btn-danger:hover,
.btn-danger:active:focus,
.btn-danger.active:focus,
.open > .dropdown-toggle.btn-danger:focus,
.btn-danger:active.focus,
.btn-danger.active.focus,
.open > .dropdown-toggle.btn-danger.focus {
  color: #fff;
  background-color: #ac2925;
  border-color: #761c19;
}
.btn-danger:active,
.btn-danger.active,
.open > .dropdown-toggle.btn-danger {
  background-image: none;
}
.btn-danger.disabled:hover,
.btn-danger[disabled]:hover,
fieldset[disabled] .btn-danger:hover,
.btn-danger.disabled:focus,
.btn-danger[disabled]:focus,
fieldset[disabled] .btn-danger:focus,
.btn-danger.disabled.focus,
.btn-danger[disabled].focus,
fieldset[disabled] .btn-danger.focus {
  background-color: #d9534f;
  border-color: #d43f3a;
}
.btn-danger .badge {
  color: #d9534f;
  background-color: #fff;
}
.btn-link {
  color: #337ab7;
  font-weight: normal;
  border-radius: 0;
}
.btn-link,
.btn-link:active,
.btn-link.active,
.btn-link[disabled],
fieldset[disabled] .btn-link {
  background-color: transparent;
  -webkit-box-shadow: none;
  box-shadow: none;
}
.btn-link,
.btn-link:hover,
.btn-link:focus,
.btn-link:active {
  border-color: transparent;
}
.btn-link:hover,
.btn-link:focus {
  color: #23527c;
  text-decoration: underline;
  background-color: transparent;
}
.btn-link[disabled]:hover,
fieldset[disabled] .btn-link:hover,
.btn-link[disabled]:focus,
fieldset[disabled] .btn-link:focus {
  color: #777777;
  text-decoration: none;
}
.btn-lg,
.btn-group-lg > .btn {
  padding: 10px 16px;
  font-size: 17px;
  line-height: 1.3333333;
  border-radius: 3px;
}
.btn-sm,
.btn-group-sm > .btn {
  padding: 5px 10px;
  font-size: 12px;
  line-height: 1.5;
  border-radius: 1px;
}
.btn-xs,
.btn-group-xs > .btn {
  padding: 1px 5px;
  font-size: 12px;
  line-height: 1.5;
  border-radius: 1px;
}
.btn-block {
  display: block;
  width: 100%;
}
.btn-block + .btn-block {
  margin-top: 5px;
}
input[type="submit"].btn-block,
input[type="reset"].btn-block,
input[type="button"].btn-block {
  width: 100%;
}
.fade {
  opacity: 0;
  -webkit-transition: opacity 0.15s linear;
  -o-transition: opacity 0.15s linear;
  transition: opacity 0.15s linear;
}
.fade.in {
  opacity: 1;
}
.collapse {
  display: none;
}
.collapse.in {
  display: block;
}
tr.collapse.in {
  display: table-row;
}
tbody.collapse.in {
  display: table-row-group;
}
.collapsing {
  position: relative;
  height: 0;
  overflow: hidden;
  -webkit-transition-property: height, visibility;
  transition-property: height, visibility;
  -webkit-transition-duration: 0.35s;
  transition-duration: 0.35s;
  -webkit-transition-timing-function: ease;
  transition-timing-function: ease;
}
.caret {
  display: inline-block;
  width: 0;
  height: 0;
  margin-left: 2px;
  vertical-align: middle;
  border-top: 4px dashed;
  border-top: 4px solid \9;
  border-right: 4px solid transparent;
  border-left: 4px solid transparent;
}
.dropup,
.dropdown {
  position: relative;
}
.dropdown-toggle:focus {
  outline: 0;
}
.dropdown-menu {
  position: absolute;
  top: 100%;
  left: 0;
  z-index: 1000;
  display: none;
  float: left;
  min-width: 160px;
  padding: 5px 0;
  margin: 2px 0 0;
  list-style: none;
  font-size: 13px;
  text-align: left;
  background-color: #fff;
  border: 1px solid #ccc;
  border: 1px solid rgba(0, 0, 0, 0.15);
  border-radius: 2px;
  -webkit-box-shadow: 0 6px 12px rgba(0, 0, 0, 0.175);
  box-shadow: 0 6px 12px rgba(0, 0, 0, 0.175);
  background-clip: padding-box;
}
.dropdown-menu.pull-right {
  right: 0;
  left: auto;
}
.dropdown-menu .divider {
  height: 1px;
  margin: 8px 0;
  overflow: hidden;
  background-color: #e5e5e5;
}
.dropdown-menu > li > a {
  display: block;
  padding: 3px 20px;
  clear: both;
  font-weight: normal;
  line-height: 1.42857143;
  color: #333333;
  white-space: nowrap;
}
.dropdown-menu > li > a:hover,
.dropdown-menu > li > a:focus {
  text-decoration: none;
  color: #262626;
  background-color: #f5f5f5;
}
.dropdown-menu > .active > a,
.dropdown-menu > .active > a:hover,
.dropdown-menu > .active > a:focus {
  color: #fff;
  text-decoration: none;
  outline: 0;
  background-color: #337ab7;
}
.dropdown-menu > .disabled > a,
.dropdown-menu > .disabled > a:hover,
.dropdown-menu > .disabled > a:focus {
  color: #777777;
}
.dropdown-menu > .disabled > a:hover,
.dropdown-menu > .disabled > a:focus {
  text-decoration: none;
  background-color: transparent;
  background-image: none;
  filter: progid:DXImageTransform.Microsoft.gradient(enabled = false);
  cursor: not-allowed;
}
.open > .dropdown-menu {
  display: block;
}
.open > a {
  outline: 0;
}
.dropdown-menu-right {
  left: auto;
  right: 0;
}
.dropdown-menu-left {
  left: 0;
  right: auto;
}
.dropdown-header {
  display: block;
  padding: 3px 20px;
  font-size: 12px;
  line-height: 1.42857143;
  color: #777777;
  white-space: nowrap;
}
.dropdown-backdrop {
  position: fixed;
  left: 0;
  right: 0;
  bottom: 0;
  top: 0;
  z-index: 990;
}
.pull-right > .dropdown-menu {
  right: 0;
  left: auto;
}
.dropup .caret,
.navbar-fixed-bottom .dropdown .caret {
  border-top: 0;
  border-bottom: 4px dashed;
  border-bottom: 4px solid \9;
  content: "";
}
.dropup .dropdown-menu,
.navbar-fixed-bottom .dropdown .dropdown-menu {
  top: auto;
  bottom: 100%;
  margin-bottom: 2px;
}
@media (min-width: 541px) {
  .navbar-right .dropdown-menu {
    left: auto;
    right: 0;
  }
  .navbar-right .dropdown-menu-left {
    left: 0;
    right: auto;
  }
}
.btn-group,
.btn-group-vertical {
  position: relative;
  display: inline-block;
  vertical-align: middle;
}
.btn-group > .btn,
.btn-group-vertical > .btn {
  position: relative;
  float: left;
}
.btn-group > .btn:hover,
.btn-group-vertical > .btn:hover,
.btn-group > .btn:focus,
.btn-group-vertical > .btn:focus,
.btn-group > .btn:active,
.btn-group-vertical > .btn:active,
.btn-group > .btn.active,
.btn-group-vertical > .btn.active {
  z-index: 2;
}
.btn-group .btn + .btn,
.btn-group .btn + .btn-group,
.btn-group .btn-group + .btn,
.btn-group .btn-group + .btn-group {
  margin-left: -1px;
}
.btn-toolbar {
  margin-left: -5px;
}
.btn-toolbar .btn,
.btn-toolbar .btn-group,
.btn-toolbar .input-group {
  float: left;
}
.btn-toolbar > .btn,
.btn-toolbar > .btn-group,
.btn-toolbar > .input-group {
  margin-left: 5px;
}
.btn-group > .btn:not(:first-child):not(:last-child):not(.dropdown-toggle) {
  border-radius: 0;
}
.btn-group > .btn:first-child {
  margin-left: 0;
}
.btn-group > .btn:first-child:not(:last-child):not(.dropdown-toggle) {
  border-bottom-right-radius: 0;
  border-top-right-radius: 0;
}
.btn-group > .btn:last-child:not(:first-child),
.btn-group > .dropdown-toggle:not(:first-child) {
  border-bottom-left-radius: 0;
  border-top-left-radius: 0;
}
.btn-group > .btn-group {
  float: left;
}
.btn-group > .btn-group:not(:first-child):not(:last-child) > .btn {
  border-radius: 0;
}
.btn-group > .btn-group:first-child:not(:last-child) > .btn:last-child,
.btn-group > .btn-group:first-child:not(:last-child) > .dropdown-toggle {
  border-bottom-right-radius: 0;
  border-top-right-radius: 0;
}
.btn-group > .btn-group:last-child:not(:first-child) > .btn:first-child {
  border-bottom-left-radius: 0;
  border-top-left-radius: 0;
}
.btn-group .dropdown-toggle:active,
.btn-group.open .dropdown-toggle {
  outline: 0;
}
.btn-group > .btn + .dropdown-toggle {
  padding-left: 8px;
  padding-right: 8px;
}
.btn-group > .btn-lg + .dropdown-toggle {
  padding-left: 12px;
  padding-right: 12px;
}
.btn-group.open .dropdown-toggle {
  -webkit-box-shadow: inset 0 3px 5px rgba(0, 0, 0, 0.125);
  box-shadow: inset 0 3px 5px rgba(0, 0, 0, 0.125);
}
.btn-group.open .dropdown-toggle.btn-link {
  -webkit-box-shadow: none;
  box-shadow: none;
}
.btn .caret {
  margin-left: 0;
}
.btn-lg .caret {
  border-width: 5px 5px 0;
  border-bottom-width: 0;
}
.dropup .btn-lg .caret {
  border-width: 0 5px 5px;
}
.btn-group-vertical > .btn,
.btn-group-vertical > .btn-group,
.btn-group-vertical > .btn-group > .btn {
  display: block;
  float: none;
  width: 100%;
  max-width: 100%;
}
.btn-group-vertical > .btn-group > .btn {
  float: none;
}
.btn-group-vertical > .btn + .btn,
.btn-group-vertical > .btn + .btn-group,
.btn-group-vertical > .btn-group + .btn,
.btn-group-vertical > .btn-group + .btn-group {
  margin-top: -1px;
  margin-left: 0;
}
.btn-group-vertical > .btn:not(:first-child):not(:last-child) {
  border-radius: 0;
}
.btn-group-vertical > .btn:first-child:not(:last-child) {
  border-top-right-radius: 2px;
  border-top-left-radius: 2px;
  border-bottom-right-radius: 0;
  border-bottom-left-radius: 0;
}
.btn-group-vertical > .btn:last-child:not(:first-child) {
  border-top-right-radius: 0;
  border-top-left-radius: 0;
  border-bottom-right-radius: 2px;
  border-bottom-left-radius: 2px;
}
.btn-group-vertical > .btn-group:not(:first-child):not(:last-child) > .btn {
  border-radius: 0;
}
.btn-group-vertical > .btn-group:first-child:not(:last-child) > .btn:last-child,
.btn-group-vertical > .btn-group:first-child:not(:last-child) > .dropdown-toggle {
  border-bottom-right-radius: 0;
  border-bottom-left-radius: 0;
}
.btn-group-vertical > .btn-group:last-child:not(:first-child) > .btn:first-child {
  border-top-right-radius: 0;
  border-top-left-radius: 0;
}
.btn-group-justified {
  display: table;
  width: 100%;
  table-layout: fixed;
  border-collapse: separate;
}
.btn-group-justified > .btn,
.btn-group-justified > .btn-group {
  float: none;
  display: table-cell;
  width: 1%;
}
.btn-group-justified > .btn-group .btn {
  width: 100%;
}
.btn-group-justified > .btn-group .dropdown-menu {
  left: auto;
}
[data-toggle="buttons"] > .btn input[type="radio"],
[data-toggle="buttons"] > .btn-group > .btn input[type="radio"],
[data-toggle="buttons"] > .btn input[type="checkbox"],
[data-toggle="buttons"] > .btn-group > .btn input[type="checkbox"] {
  position: absolute;
  clip: rect(0, 0, 0, 0);
  pointer-events: none;
}
.input-group {
  position: relative;
  display: table;
  border-collapse: separate;
}
.input-group[class*="col-"] {
  float: none;
  padding-left: 0;
  padding-right: 0;
}
.input-group .form-control {
  position: relative;
  z-index: 2;
  float: left;
  width: 100%;
  margin-bottom: 0;
}
.input-group .form-control:focus {
  z-index: 3;
}
.input-group-lg > .form-control,
.input-group-lg > .input-group-addon,
.input-group-lg > .input-group-btn > .btn {
  height: 45px;
  padding: 10px 16px;
  font-size: 17px;
  line-height: 1.3333333;
  border-radius: 3px;
}
select.input-group-lg > .form-control,
select.input-group-lg > .input-group-addon,
select.input-group-lg > .input-group-btn > .btn {
  height: 45px;
  line-height: 45px;
}
textarea.input-group-lg > .form-control,
textarea.input-group-lg > .input-group-addon,
textarea.input-group-lg > .input-group-btn > .btn,
select[multiple].input-group-lg > .form-control,
select[multiple].input-group-lg > .input-group-addon,
select[multiple].input-group-lg > .input-group-btn > .btn {
  height: auto;
}
.input-group-sm > .form-control,
.input-group-sm > .input-group-addon,
.input-group-sm > .input-group-btn > .btn {
  height: 30px;
  padding: 5px 10px;
  font-size: 12px;
  line-height: 1.5;
  border-radius: 1px;
}
select.input-group-sm > .form-control,
select.input-group-sm > .input-group-addon,
select.input-group-sm > .input-group-btn > .btn {
  height: 30px;
  line-height: 30px;
}
textarea.input-group-sm > .form-control,
textarea.input-group-sm > .input-group-addon,
textarea.input-group-sm > .input-group-btn > .btn,
select[multiple].input-group-sm > .form-control,
select[multiple].input-group-sm > .input-group-addon,
select[multiple].input-group-sm > .input-group-btn > .btn {
  height: auto;
}
.input-group-addon,
.input-group-btn,
.input-group .form-control {
  display: table-cell;
}
.input-group-addon:not(:first-child):not(:last-child),
.input-group-btn:not(:first-child):not(:last-child),
.input-group .form-control:not(:first-child):not(:last-child) {
  border-radius: 0;
}
.input-group-addon,
.input-group-btn {
  width: 1%;
  white-space: nowrap;
  vertical-align: middle;
}
.input-group-addon {
  padding: 6px 12px;
  font-size: 13px;
  font-weight: normal;
  line-height: 1;
  color: #555555;
  text-align: center;
  background-color: #eeeeee;
  border: 1px solid #ccc;
  border-radius: 2px;
}
.input-group-addon.input-sm {
  padding: 5px 10px;
  font-size: 12px;
  border-radius: 1px;
}
.input-group-addon.input-lg {
  padding: 10px 16px;
  font-size: 17px;
  border-radius: 3px;
}
.input-group-addon input[type="radio"],
.input-group-addon input[type="checkbox"] {
  margin-top: 0;
}
.input-group .form-control:first-child,
.input-group-addon:first-child,
.input-group-btn:first-child > .btn,
.input-group-btn:first-child > .btn-group > .btn,
.input-group-btn:first-child > .dropdown-toggle,
.input-group-btn:last-child > .btn:not(:last-child):not(.dropdown-toggle),
.input-group-btn:last-child > .btn-group:not(:last-child) > .btn {
  border-bottom-right-radius: 0;
  border-top-right-radius: 0;
}
.input-group-addon:first-child {
  border-right: 0;
}
.input-group .form-control:last-child,
.input-group-addon:last-child,
.input-group-btn:last-child > .btn,
.input-group-btn:last-child > .btn-group > .btn,
.input-group-btn:last-child > .dropdown-toggle,
.input-group-btn:first-child > .btn:not(:first-child),
.input-group-btn:first-child > .btn-group:not(:first-child) > .btn {
  border-bottom-left-radius: 0;
  border-top-left-radius: 0;
}
.input-group-addon:last-child {
  border-left: 0;
}
.input-group-btn {
  position: relative;
  font-size: 0;
  white-space: nowrap;
}
.input-group-btn > .btn {
  position: relative;
}
.input-group-btn > .btn + .btn {
  margin-left: -1px;
}
.input-group-btn > .btn:hover,
.input-group-btn > .btn:focus,
.input-group-btn > .btn:active {
  z-index: 2;
}
.input-group-btn:first-child > .btn,
.input-group-btn:first-child > .btn-group {
  margin-right: -1px;
}
.input-group-btn:last-child > .btn,
.input-group-btn:last-child > .btn-group {
  z-index: 2;
  margin-left: -1px;
}
.nav {
  margin-bottom: 0;
  padding-left: 0;
  list-style: none;
}
.nav > li {
  position: relative;
  display: block;
}
.nav > li > a {
  position: relative;
  display: block;
  padding: 10px 15px;
}
.nav > li > a:hover,
.nav > li > a:focus {
  text-decoration: none;
  background-color: #eeeeee;
}
.nav > li.disabled > a {
  color: #777777;
}
.nav > li.disabled > a:hover,
.nav > li.disabled > a:focus {
  color: #777777;
  text-decoration: none;
  background-color: transparent;
  cursor: not-allowed;
}
.nav .open > a,
.nav .open > a:hover,
.nav .open > a:focus {
  background-color: #eeeeee;
  border-color: #337ab7;
}
.nav .nav-divider {
  height: 1px;
  margin: 8px 0;
  overflow: hidden;
  background-color: #e5e5e5;
}
.nav > li > a > img {
  max-width: none;
}
.nav-tabs {
  border-bottom: 1px solid #ddd;
}
.nav-tabs > li {
  float: left;
  margin-bottom: -1px;
}
.nav-tabs > li > a {
  margin-right: 2px;
  line-height: 1.42857143;
  border: 1px solid transparent;
  border-radius: 2px 2px 0 0;
}
.nav-tabs > li > a:hover {
  border-color: #eeeeee #eeeeee #ddd;
}
.nav-tabs > li.active > a,
.nav-tabs > li.active > a:hover,
.nav-tabs > li.active > a:focus {
  color: #555555;
  background-color: #fff;
  border: 1px solid #ddd;
  border-bottom-color: transparent;
  cursor: default;
}
.nav-tabs.nav-justified {
  width: 100%;
  border-bottom: 0;
}
.nav-tabs.nav-justified > li {
  float: none;
}
.nav-tabs.nav-justified > li > a {
  text-align: center;
  margin-bottom: 5px;
}
.nav-tabs.nav-justified > .dropdown .dropdown-menu {
  top: auto;
  left: auto;
}
@media (min-width: 768px) {
  .nav-tabs.nav-justified > li {
    display: table-cell;
    width: 1%;
  }
  .nav-tabs.nav-justified > li > a {
    margin-bottom: 0;
  }
}
.nav-tabs.nav-justified > li > a {
  margin-right: 0;
  border-radius: 2px;
}
.nav-tabs.nav-justified > .active > a,
.nav-tabs.nav-justified > .active > a:hover,
.nav-tabs.nav-justified > .active > a:focus {
  border: 1px solid #ddd;
}
@media (min-width: 768px) {
  .nav-tabs.nav-justified > li > a {
    border-bottom: 1px solid #ddd;
    border-radius: 2px 2px 0 0;
  }
  .nav-tabs.nav-justified > .active > a,
  .nav-tabs.nav-justified > .active > a:hover,
  .nav-tabs.nav-justified > .active > a:focus {
    border-bottom-color: #fff;
  }
}
.nav-pills > li {
  float: left;
}
.nav-pills > li > a {
  border-radius: 2px;
}
.nav-pills > li + li {
  margin-left: 2px;
}
.nav-pills > li.active > a,
.nav-pills > li.active > a:hover,
.nav-pills > li.active > a:focus {
  color: #fff;
  background-color: #337ab7;
}
.nav-stacked > li {
  float: none;
}
.nav-stacked > li + li {
  margin-top: 2px;
  margin-left: 0;
}
.nav-justified {
  width: 100%;
}
.nav-justified > li {
  float: none;
}
.nav-justified > li > a {
  text-align: center;
  margin-bottom: 5px;
}
.nav-justified > .dropdown .dropdown-menu {
  top: auto;
  left: auto;
}
@media (min-width: 768px) {
  .nav-justified > li {
    display: table-cell;
    width: 1%;
  }
  .nav-justified > li > a {
    margin-bottom: 0;
  }
}
.nav-tabs-justified {
  border-bottom: 0;
}
.nav-tabs-justified > li > a {
  margin-right: 0;
  border-radius: 2px;
}
.nav-tabs-justified > .active > a,
.nav-tabs-justified > .active > a:hover,
.nav-tabs-justified > .active > a:focus {
  border: 1px solid #ddd;
}
@media (min-width: 768px) {
  .nav-tabs-justified > li > a {
    border-bottom: 1px solid #ddd;
    border-radius: 2px 2px 0 0;
  }
  .nav-tabs-justified > .active > a,
  .nav-tabs-justified > .active > a:hover,
  .nav-tabs-justified > .active > a:focus {
    border-bottom-color: #fff;
  }
}
.tab-content > .tab-pane {
  display: none;
}
.tab-content > .active {
  display: block;
}
.nav-tabs .dropdown-menu {
  margin-top: -1px;
  border-top-right-radius: 0;
  border-top-left-radius: 0;
}
.navbar {
  position: relative;
  min-height: 30px;
  margin-bottom: 18px;
  border: 1px solid transparent;
}
@media (min-width: 541px) {
  .navbar {
    border-radius: 2px;
  }
}
@media (min-width: 541px) {
  .navbar-header {
    float: left;
  }
}
.navbar-collapse {
  overflow-x: visible;
  padding-right: 0px;
  padding-left: 0px;
  border-top: 1px solid transparent;
  box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.1);
  -webkit-overflow-scrolling: touch;
}
.navbar-collapse.in {
  overflow-y: auto;
}
@media (min-width: 541px) {
  .navbar-collapse {
    width: auto;
    border-top: 0;
    box-shadow: none;
  }
  .navbar-collapse.collapse {
    display: block !important;
    height: auto !important;
    padding-bottom: 0;
    overflow: visible !important;
  }
  .navbar-collapse.in {
    overflow-y: visible;
  }
  .navbar-fixed-top .navbar-collapse,
  .navbar-static-top .navbar-collapse,
  .navbar-fixed-bottom .navbar-collapse {
    padding-left: 0;
    padding-right: 0;
  }
}
.navbar-fixed-top .navbar-collapse,
.navbar-fixed-bottom .navbar-collapse {
  max-height: 340px;
}
@media (max-device-width: 540px) and (orientation: landscape) {
  .navbar-fixed-top .navbar-collapse,
  .navbar-fixed-bottom .navbar-collapse {
    max-height: 200px;
  }
}
.container > .navbar-header,
.container-fluid > .navbar-header,
.container > .navbar-collapse,
.container-fluid > .navbar-collapse {
  margin-right: 0px;
  margin-left: 0px;
}
@media (min-width: 541px) {
  .container > .navbar-header,
  .container-fluid > .navbar-header,
  .container > .navbar-collapse,
  .container-fluid > .navbar-collapse {
    margin-right: 0;
    margin-left: 0;
  }
}
.navbar-static-top {
  z-index: 1000;
  border-width: 0 0 1px;
}
@media (min-width: 541px) {
  .navbar-static-top {
    border-radius: 0;
  }
}
.navbar-fixed-top,
.navbar-fixed-bottom {
  position: fixed;
  right: 0;
  left: 0;
  z-index: 1030;
}
@media (min-width: 541px) {
  .navbar-fixed-top,
  .navbar-fixed-bottom {
    border-radius: 0;
  }
}
.navbar-fixed-top {
  top: 0;
  border-width: 0 0 1px;
}
.navbar-fixed-bottom {
  bottom: 0;
  margin-bottom: 0;
  border-width: 1px 0 0;
}
.navbar-brand {
  float: left;
  padding: 6px 0px;
  font-size: 17px;
  line-height: 18px;
  height: 30px;
}
.navbar-brand:hover,
.navbar-brand:focus {
  text-decoration: none;
}
.navbar-brand > img {
  display: block;
}
@media (min-width: 541px) {
  .navbar > .container .navbar-brand,
  .navbar > .container-fluid .navbar-brand {
    margin-left: 0px;
  }
}
.navbar-toggle {
  position: relative;
  float: right;
  margin-right: 0px;
  padding: 9px 10px;
  margin-top: -2px;
  margin-bottom: -2px;
  background-color: transparent;
  background-image: none;
  border: 1px solid transparent;
  border-radius: 2px;
}
.navbar-toggle:focus {
  outline: 0;
}
.navbar-toggle .icon-bar {
  display: block;
  width: 22px;
  height: 2px;
  border-radius: 1px;
}
.navbar-toggle .icon-bar + .icon-bar {
  margin-top: 4px;
}
@media (min-width: 541px) {
  .navbar-toggle {
    display: none;
  }
}
.navbar-nav {
  margin: 3px 0px;
}
.navbar-nav > li > a {
  padding-top: 10px;
  padding-bottom: 10px;
  line-height: 18px;
}
@media (max-width: 540px) {
  .navbar-nav .open .dropdown-menu {
    position: static;
    float: none;
    width: auto;
    margin-top: 0;
    background-color: transparent;
    border: 0;
    box-shadow: none;
  }
  .navbar-nav .open .dropdown-menu > li > a,
  .navbar-nav .open .dropdown-menu .dropdown-header {
    padding: 5px 15px 5px 25px;
  }
  .navbar-nav .open .dropdown-menu > li > a {
    line-height: 18px;
  }
  .navbar-nav .open .dropdown-menu > li > a:hover,
  .navbar-nav .open .dropdown-menu > li > a:focus {
    background-image: none;
  }
}
@media (min-width: 541px) {
  .navbar-nav {
    float: left;
    margin: 0;
  }
  .navbar-nav > li {
    float: left;
  }
  .navbar-nav > li > a {
    padding-top: 6px;
    padding-bottom: 6px;
  }
}
.navbar-form {
  margin-left: 0px;
  margin-right: 0px;
  padding: 10px 0px;
  border-top: 1px solid transparent;
  border-bottom: 1px solid transparent;
  -webkit-box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.1), 0 1px 0 rgba(255, 255, 255, 0.1);
  box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.1), 0 1px 0 rgba(255, 255, 255, 0.1);
  margin-top: -1px;
  margin-bottom: -1px;
}
@media (min-width: 768px) {
  .navbar-form .form-group {
    display: inline-block;
    margin-bottom: 0;
    vertical-align: middle;
  }
  .navbar-form .form-control {
    display: inline-block;
    width: auto;
    vertical-align: middle;
  }
  .navbar-form .form-control-static {
    display: inline-block;
  }
  .navbar-form .input-group {
    display: inline-table;
    vertical-align: middle;
  }
  .navbar-form .input-group .input-group-addon,
  .navbar-form .input-group .input-group-btn,
  .navbar-form .input-group .form-control {
    width: auto;
  }
  .navbar-form .input-group > .form-control {
    width: 100%;
  }
  .navbar-form .control-label {
    margin-bottom: 0;
    vertical-align: middle;
  }
  .navbar-form .radio,
  .navbar-form .checkbox {
    display: inline-block;
    margin-top: 0;
    margin-bottom: 0;
    vertical-align: middle;
  }
  .navbar-form .radio label,
  .navbar-form .checkbox label {
    padding-left: 0;
  }
  .navbar-form .radio input[type="radio"],
  .navbar-form .checkbox input[type="checkbox"] {
    position: relative;
    margin-left: 0;
  }
  .navbar-form .has-feedback .form-control-feedback {
    top: 0;
  }
}
@media (max-width: 540px) {
  .navbar-form .form-group {
    margin-bottom: 5px;
  }
  .navbar-form .form-group:last-child {
    margin-bottom: 0;
  }
}
@media (min-width: 541px) {
  .navbar-form {
    width: auto;
    border: 0;
    margin-left: 0;
    margin-right: 0;
    padding-top: 0;
    padding-bottom: 0;
    -webkit-box-shadow: none;
    box-shadow: none;
  }
}
.navbar-nav > li > .dropdown-menu {
  margin-top: 0;
  border-top-right-radius: 0;
  border-top-left-radius: 0;
}
.navbar-fixed-bottom .navbar-nav > li > .dropdown-menu {
  margin-bottom: 0;
  border-top-right-radius: 2px;
  border-top-left-radius: 2px;
  border-bottom-right-radius: 0;
  border-bottom-left-radius: 0;
}
.navbar-btn {
  margin-top: -1px;
  margin-bottom: -1px;
}
.navbar-btn.btn-sm {
  margin-top: 0px;
  margin-bottom: 0px;
}
.navbar-btn.btn-xs {
  margin-top: 4px;
  margin-bottom: 4px;
}
.navbar-text {
  margin-top: 6px;
  margin-bottom: 6px;
}
@media (min-width: 541px) {
  .navbar-text {
    float: left;
    margin-left: 0px;
    margin-right: 0px;
  }
}
@media (min-width: 541px) {
  .navbar-left {
    float: left !important;
    float: left;
  }
  .navbar-right {
    float: right !important;
    float: right;
    margin-right: 0px;
  }
  .navbar-right ~ .navbar-right {
    margin-right: 0;
  }
}
.navbar-default {
  background-color: #f8f8f8;
  border-color: #e7e7e7;
}
.navbar-default .navbar-brand {
  color: #777;
}
.navbar-default .navbar-brand:hover,
.navbar-default .navbar-brand:focus {
  color: #5e5e5e;
  background-color: transparent;
}
.navbar-default .navbar-text {
  color: #777;
}
.navbar-default .navbar-nav > li > a {
  color: #777;
}
.navbar-default .navbar-nav > li > a:hover,
.navbar-default .navbar-nav > li > a:focus {
  color: #333;
  background-color: transparent;
}
.navbar-default .navbar-nav > .active > a,
.navbar-default .navbar-nav > .active > a:hover,
.navbar-default .navbar-nav > .active > a:focus {
  color: #555;
  background-color: #e7e7e7;
}
.navbar-default .navbar-nav > .disabled > a,
.navbar-default .navbar-nav > .disabled > a:hover,
.navbar-default .navbar-nav > .disabled > a:focus {
  color: #ccc;
  background-color: transparent;
}
.navbar-default .navbar-toggle {
  border-color: #ddd;
}
.navbar-default .navbar-toggle:hover,
.navbar-default .navbar-toggle:focus {
  background-color: #ddd;
}
.navbar-default .navbar-toggle .icon-bar {
  background-color: #888;
}
.navbar-default .navbar-collapse,
.navbar-default .navbar-form {
  border-color: #e7e7e7;
}
.navbar-default .navbar-nav > .open > a,
.navbar-default .navbar-nav > .open > a:hover,
.navbar-default .navbar-nav > .open > a:focus {
  background-color: #e7e7e7;
  color: #555;
}
@media (max-width: 540px) {
  .navbar-default .navbar-nav .open .dropdown-menu > li > a {
    color: #777;
  }
  .navbar-default .navbar-nav .open .dropdown-menu > li > a:hover,
  .navbar-default .navbar-nav .open .dropdown-menu > li > a:focus {
    color: #333;
    background-color: transparent;
  }
  .navbar-default .navbar-nav .open .dropdown-menu > .active > a,
  .navbar-default .navbar-nav .open .dropdown-menu > .active > a:hover,
  .navbar-default .navbar-nav .open .dropdown-menu > .active > a:focus {
    color: #555;
    background-color: #e7e7e7;
  }
  .navbar-default .navbar-nav .open .dropdown-menu > .disabled > a,
  .navbar-default .navbar-nav .open .dropdown-menu > .disabled > a:hover,
  .navbar-default .navbar-nav .open .dropdown-menu > .disabled > a:focus {
    color: #ccc;
    background-color: transparent;
  }
}
.navbar-default .navbar-link {
  color: #777;
}
.navbar-default .navbar-link:hover {
  color: #333;
}
.navbar-default .btn-link {
  color: #777;
}
.navbar-default .btn-link:hover,
.navbar-default .btn-link:focus {
  color: #333;
}
.navbar-default .btn-link[disabled]:hover,
fieldset[disabled] .navbar-default .btn-link:hover,
.navbar-default .btn-link[disabled]:focus,
fieldset[disabled] .navbar-default .btn-link:focus {
  color: #ccc;
}
.navbar-inverse {
  background-color: #222;
  border-color: #080808;
}
.navbar-inverse .navbar-brand {
  color: #9d9d9d;
}
.navbar-inverse .navbar-brand:hover,
.navbar-inverse .navbar-brand:focus {
  color: #fff;
  background-color: transparent;
}
.navbar-inverse .navbar-text {
  color: #9d9d9d;
}
.navbar-inverse .navbar-nav > li > a {
  color: #9d9d9d;
}
.navbar-inverse .navbar-nav > li > a:hover,
.navbar-inverse .navbar-nav > li > a:focus {
  color: #fff;
  background-color: transparent;
}
.navbar-inverse .navbar-nav > .active > a,
.navbar-inverse .navbar-nav > .active > a:hover,
.navbar-inverse .navbar-nav > .active > a:focus {
  color: #fff;
  background-color: #080808;
}
.navbar-inverse .navbar-nav > .disabled > a,
.navbar-inverse .navbar-nav > .disabled > a:hover,
.navbar-inverse .navbar-nav > .disabled > a:focus {
  color: #444;
  background-color: transparent;
}
.navbar-inverse .navbar-toggle {
  border-color: #333;
}
.navbar-inverse .navbar-toggle:hover,
.navbar-inverse .navbar-toggle:focus {
  background-color: #333;
}
.navbar-inverse .navbar-toggle .icon-bar {
  background-color: #fff;
}
.navbar-inverse .navbar-collapse,
.navbar-inverse .navbar-form {
  border-color: #101010;
}
.navbar-inverse .navbar-nav > .open > a,
.navbar-inverse .navbar-nav > .open > a:hover,
.navbar-inverse .navbar-nav > .open > a:focus {
  background-color: #080808;
  color: #fff;
}
@media (max-width: 540px) {
  .navbar-inverse .navbar-nav .open .dropdown-menu > .dropdown-header {
    border-color: #080808;
  }
  .navbar-inverse .navbar-nav .open .dropdown-menu .divider {
    background-color: #080808;
  }
  .navbar-inverse .navbar-nav .open .dropdown-menu > li > a {
    color: #9d9d9d;
  }
  .navbar-inverse .navbar-nav .open .dropdown-menu > li > a:hover,
  .navbar-inverse .navbar-nav .open .dropdown-menu > li > a:focus {
    color: #fff;
    background-color: transparent;
  }
  .navbar-inverse .navbar-nav .open .dropdown-menu > .active > a,
  .navbar-inverse .navbar-nav .open .dropdown-menu > .active > a:hover,
  .navbar-inverse .navbar-nav .open .dropdown-menu > .active > a:focus {
    color: #fff;
    background-color: #080808;
  }
  .navbar-inverse .navbar-nav .open .dropdown-menu > .disabled > a,
  .navbar-inverse .navbar-nav .open .dropdown-menu > .disabled > a:hover,
  .navbar-inverse .navbar-nav .open .dropdown-menu > .disabled > a:focus {
    color: #444;
    background-color: transparent;
  }
}
.navbar-inverse .navbar-link {
  color: #9d9d9d;
}
.navbar-inverse .navbar-link:hover {
  color: #fff;
}
.navbar-inverse .btn-link {
  color: #9d9d9d;
}
.navbar-inverse .btn-link:hover,
.navbar-inverse .btn-link:focus {
  color: #fff;
}
.navbar-inverse .btn-link[disabled]:hover,
fieldset[disabled] .navbar-inverse .btn-link:hover,
.navbar-inverse .btn-link[disabled]:focus,
fieldset[disabled] .navbar-inverse .btn-link:focus {
  color: #444;
}
.breadcrumb {
  padding: 8px 15px;
  margin-bottom: 18px;
  list-style: none;
  background-color: #f5f5f5;
  border-radius: 2px;
}
.breadcrumb > li {
  display: inline-block;
}
.breadcrumb > li + li:before {
  content: "/\00a0";
  padding: 0 5px;
  color: #5e5e5e;
}
.breadcrumb > .active {
  color: #777777;
}
.pagination {
  display: inline-block;
  padding-left: 0;
  margin: 18px 0;
  border-radius: 2px;
}
.pagination > li {
  display: inline;
}
.pagination > li > a,
.pagination > li > span {
  position: relative;
  float: left;
  padding: 6px 12px;
  line-height: 1.42857143;
  text-decoration: none;
  color: #337ab7;
  background-color: #fff;
  border: 1px solid #ddd;
  margin-left: -1px;
}
.pagination > li:first-child > a,
.pagination > li:first-child > span {
  margin-left: 0;
  border-bottom-left-radius: 2px;
  border-top-left-radius: 2px;
}
.pagination > li:last-child > a,
.pagination > li:last-child > span {
  border-bottom-right-radius: 2px;
  border-top-right-radius: 2px;
}
.pagination > li > a:hover,
.pagination > li > span:hover,
.pagination > li > a:focus,
.pagination > li > span:focus {
  z-index: 2;
  color: #23527c;
  background-color: #eeeeee;
  border-color: #ddd;
}
.pagination > .active > a,
.pagination > .active > span,
.pagination > .active > a:hover,
.pagination > .active > span:hover,
.pagination > .active > a:focus,
.pagination > .active > span:focus {
  z-index: 3;
  color: #fff;
  background-color: #337ab7;
  border-color: #337ab7;
  cursor: default;
}
.pagination > .disabled > span,
.pagination > .disabled > span:hover,
.pagination > .disabled > span:focus,
.pagination > .disabled > a,
.pagination > .disabled > a:hover,
.pagination > .disabled > a:focus {
  color: #777777;
  background-color: #fff;
  border-color: #ddd;
  cursor: not-allowed;
}
.pagination-lg > li > a,
.pagination-lg > li > span {
  padding: 10px 16px;
  font-size: 17px;
  line-height: 1.3333333;
}
.pagination-lg > li:first-child > a,
.pagination-lg > li:first-child > span {
  border-bottom-left-radius: 3px;
  border-top-left-radius: 3px;
}
.pagination-lg > li:last-child > a,
.pagination-lg > li:last-child > span {
  border-bottom-right-radius: 3px;
  border-top-right-radius: 3px;
}
.pagination-sm > li > a,
.pagination-sm > li > span {
  padding: 5px 10px;
  font-size: 12px;
  line-height: 1.5;
}
.pagination-sm > li:first-child > a,
.pagination-sm > li:first-child > span {
  border-bottom-left-radius: 1px;
  border-top-left-radius: 1px;
}
.pagination-sm > li:last-child > a,
.pagination-sm > li:last-child > span {
  border-bottom-right-radius: 1px;
  border-top-right-radius: 1px;
}
.pager {
  padding-left: 0;
  margin: 18px 0;
  list-style: none;
  text-align: center;
}
.pager li {
  display: inline;
}
.pager li > a,
.pager li > span {
  display: inline-block;
  padding: 5px 14px;
  background-color: #fff;
  border: 1px solid #ddd;
  border-radius: 15px;
}
.pager li > a:hover,
.pager li > a:focus {
  text-decoration: none;
  background-color: #eeeeee;
}
.pager .next > a,
.pager .next > span {
  float: right;
}
.pager .previous > a,
.pager .previous > span {
  float: left;
}
.pager .disabled > a,
.pager .disabled > a:hover,
.pager .disabled > a:focus,
.pager .disabled > span {
  color: #777777;
  background-color: #fff;
  cursor: not-allowed;
}
.label {
  display: inline;
  padding: .2em .6em .3em;
  font-size: 75%;
  font-weight: bold;
  line-height: 1;
  color: #fff;
  text-align: center;
  white-space: nowrap;
  vertical-align: baseline;
  border-radius: .25em;
}
a.label:hover,
a.label:focus {
  color: #fff;
  text-decoration: none;
  cursor: pointer;
}
.label:empty {
  display: none;
}
.btn .label {
  position: relative;
  top: -1px;
}
.label-default {
  background-color: #777777;
}
.label-default[href]:hover,
.label-default[href]:focus {
  background-color: #5e5e5e;
}
.label-primary {
  background-color: #337ab7;
}
.label-primary[href]:hover,
.label-primary[href]:focus {
  background-color: #286090;
}
.label-success {
  background-color: #5cb85c;
}
.label-success[href]:hover,
.label-success[href]:focus {
  background-color: #449d44;
}
.label-info {
  background-color: #5bc0de;
}
.label-info[href]:hover,
.label-info[href]:focus {
  background-color: #31b0d5;
}
.label-warning {
  background-color: #f0ad4e;
}
.label-warning[href]:hover,
.label-warning[href]:focus {
  background-color: #ec971f;
}
.label-danger {
  background-color: #d9534f;
}
.label-danger[href]:hover,
.label-danger[href]:focus {
  background-color: #c9302c;
}
.badge {
  display: inline-block;
  min-width: 10px;
  padding: 3px 7px;
  font-size: 12px;
  font-weight: bold;
  color: #fff;
  line-height: 1;
  vertical-align: middle;
  white-space: nowrap;
  text-align: center;
  background-color: #777777;
  border-radius: 10px;
}
.badge:empty {
  display: none;
}
.btn .badge {
  position: relative;
  top: -1px;
}
.btn-xs .badge,
.btn-group-xs > .btn .badge {
  top: 0;
  padding: 1px 5px;
}
a.badge:hover,
a.badge:focus {
  color: #fff;
  text-decoration: none;
  cursor: pointer;
}
.list-group-item.active > .badge,
.nav-pills > .active > a > .badge {
  color: #337ab7;
  background-color: #fff;
}
.list-group-item > .badge {
  float: right;
}
.list-group-item > .badge + .badge {
  margin-right: 5px;
}
.nav-pills > li > a > .badge {
  margin-left: 3px;
}
.jumbotron {
  padding-top: 30px;
  padding-bottom: 30px;
  margin-bottom: 30px;
  color: inherit;
  background-color: #eeeeee;
}
.jumbotron h1,
.jumbotron .h1 {
  color: inherit;
}
.jumbotron p {
  margin-bottom: 15px;
  font-size: 20px;
  font-weight: 200;
}
.jumbotron > hr {
  border-top-color: #d5d5d5;
}
.container .jumbotron,
.container-fluid .jumbotron {
  border-radius: 3px;
  padding-left: 0px;
  padding-right: 0px;
}
.jumbotron .container {
  max-width: 100%;
}
@media screen and (min-width: 768px) {
  .jumbotron {
    padding-top: 48px;
    padding-bottom: 48px;
  }
  .container .jumbotron,
  .container-fluid .jumbotron {
    padding-left: 60px;
    padding-right: 60px;
  }
  .jumbotron h1,
  .jumbotron .h1 {
    font-size: 59px;
  }
}
.thumbnail {
  display: block;
  padding: 4px;
  margin-bottom: 18px;
  line-height: 1.42857143;
  background-color: #fff;
  border: 1px solid #ddd;
  border-radius: 2px;
  -webkit-transition: border 0.2s ease-in-out;
  -o-transition: border 0.2s ease-in-out;
  transition: border 0.2s ease-in-out;
}
.thumbnail > img,
.thumbnail a > img {
  margin-left: auto;
  margin-right: auto;
}
a.thumbnail:hover,
a.thumbnail:focus,
a.thumbnail.active {
  border-color: #337ab7;
}
.thumbnail .caption {
  padding: 9px;
  color: #000;
}
.alert {
  padding: 15px;
  margin-bottom: 18px;
  border: 1px solid transparent;
  border-radius: 2px;
}
.alert h4 {
  margin-top: 0;
  color: inherit;
}
.alert .alert-link {
  font-weight: bold;
}
.alert > p,
.alert > ul {
  margin-bottom: 0;
}
.alert > p + p {
  margin-top: 5px;
}
.alert-dismissable,
.alert-dismissible {
  padding-right: 35px;
}
.alert-dismissable .close,
.alert-dismissible .close {
  position: relative;
  top: -2px;
  right: -21px;
  color: inherit;
}
.alert-success {
  background-color: #dff0d8;
  border-color: #d6e9c6;
  color: #3c763d;
}
.alert-success hr {
  border-top-color: #c9e2b3;
}
.alert-success .alert-link {
  color: #2b542c;
}
.alert-info {
  background-color: #d9edf7;
  border-color: #bce8f1;
  color: #31708f;
}
.alert-info hr {
  border-top-color: #a6e1ec;
}
.alert-info .alert-link {
  color: #245269;
}
.alert-warning {
  background-color: #fcf8e3;
  border-color: #faebcc;
  color: #8a6d3b;
}
.alert-warning hr {
  border-top-color: #f7e1b5;
}
.alert-warning .alert-link {
  color: #66512c;
}
.alert-danger {
  background-color: #f2dede;
  border-color: #ebccd1;
  color: #a94442;
}
.alert-danger hr {
  border-top-color: #e4b9c0;
}
.alert-danger .alert-link {
  color: #843534;
}
@-webkit-keyframes progress-bar-stripes {
  from {
    background-position: 40px 0;
  }
  to {
    background-position: 0 0;
  }
}
@keyframes progress-bar-stripes {
  from {
    background-position: 40px 0;
  }
  to {
    background-position: 0 0;
  }
}
.progress {
  overflow: hidden;
  height: 18px;
  margin-bottom: 18px;
  background-color: #f5f5f5;
  border-radius: 2px;
  -webkit-box-shadow: inset 0 1px 2px rgba(0, 0, 0, 0.1);
  box-shadow: inset 0 1px 2px rgba(0, 0, 0, 0.1);
}
.progress-bar {
  float: left;
  width: 0%;
  height: 100%;
  font-size: 12px;
  line-height: 18px;
  color: #fff;
  text-align: center;
  background-color: #337ab7;
  -webkit-box-shadow: inset 0 -1px 0 rgba(0, 0, 0, 0.15);
  box-shadow: inset 0 -1px 0 rgba(0, 0, 0, 0.15);
  -webkit-transition: width 0.6s ease;
  -o-transition: width 0.6s ease;
  transition: width 0.6s ease;
}
.progress-striped .progress-bar,
.progress-bar-striped {
  background-image: -webkit-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);
  background-image: -o-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);
  background-image: linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);
  background-size: 40px 40px;
}
.progress.active .progress-bar,
.progress-bar.active {
  -webkit-animation: progress-bar-stripes 2s linear infinite;
  -o-animation: progress-bar-stripes 2s linear infinite;
  animation: progress-bar-stripes 2s linear infinite;
}
.progress-bar-success {
  background-color: #5cb85c;
}
.progress-striped .progress-bar-success {
  background-image: -webkit-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);
  background-image: -o-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);
  background-image: linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);
}
.progress-bar-info {
  background-color: #5bc0de;
}
.progress-striped .progress-bar-info {
  background-image: -webkit-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);
  background-image: -o-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);
  background-image: linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);
}
.progress-bar-warning {
  background-color: #f0ad4e;
}
.progress-striped .progress-bar-warning {
  background-image: -webkit-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);
  background-image: -o-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);
  background-image: linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);
}
.progress-bar-danger {
  background-color: #d9534f;
}
.progress-striped .progress-bar-danger {
  background-image: -webkit-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);
  background-image: -o-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);
  background-image: linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);
}
.media {
  margin-top: 15px;
}
.media:first-child {
  margin-top: 0;
}
.media,
.media-body {
  zoom: 1;
  overflow: hidden;
}
.media-body {
  width: 10000px;
}
.media-object {
  display: block;
}
.media-object.img-thumbnail {
  max-width: none;
}
.media-right,
.media > .pull-right {
  padding-left: 10px;
}
.media-left,
.media > .pull-left {
  padding-right: 10px;
}
.media-left,
.media-right,
.media-body {
  display: table-cell;
  vertical-align: top;
}
.media-middle {
  vertical-align: middle;
}
.media-bottom {
  vertical-align: bottom;
}
.media-heading {
  margin-top: 0;
  margin-bottom: 5px;
}
.media-list {
  padding-left: 0;
  list-style: none;
}
.list-group {
  margin-bottom: 20px;
  padding-left: 0;
}
.list-group-item {
  position: relative;
  display: block;
  padding: 10px 15px;
  margin-bottom: -1px;
  background-color: #fff;
  border: 1px solid #ddd;
}
.list-group-item:first-child {
  border-top-right-radius: 2px;
  border-top-left-radius: 2px;
}
.list-group-item:last-child {
  margin-bottom: 0;
  border-bottom-right-radius: 2px;
  border-bottom-left-radius: 2px;
}
a.list-group-item,
button.list-group-item {
  color: #555;
}
a.list-group-item .list-group-item-heading,
button.list-group-item .list-group-item-heading {
  color: #333;
}
a.list-group-item:hover,
button.list-group-item:hover,
a.list-group-item:focus,
button.list-group-item:focus {
  text-decoration: none;
  color: #555;
  background-color: #f5f5f5;
}
button.list-group-item {
  width: 100%;
  text-align: left;
}
.list-group-item.disabled,
.list-group-item.disabled:hover,
.list-group-item.disabled:focus {
  background-color: #eeeeee;
  color: #777777;
  cursor: not-allowed;
}
.list-group-item.disabled .list-group-item-heading,
.list-group-item.disabled:hover .list-group-item-heading,
.list-group-item.disabled:focus .list-group-item-heading {
  color: inherit;
}
.list-group-item.disabled .list-group-item-text,
.list-group-item.disabled:hover .list-group-item-text,
.list-group-item.disabled:focus .list-group-item-text {
  color: #777777;
}
.list-group-item.active,
.list-group-item.active:hover,
.list-group-item.active:focus {
  z-index: 2;
  color: #fff;
  background-color: #337ab7;
  border-color: #337ab7;
}
.list-group-item.active .list-group-item-heading,
.list-group-item.active:hover .list-group-item-heading,
.list-group-item.active:focus .list-group-item-heading,
.list-group-item.active .list-group-item-heading > small,
.list-group-item.active:hover .list-group-item-heading > small,
.list-group-item.active:focus .list-group-item-heading > small,
.list-group-item.active .list-group-item-heading > .small,
.list-group-item.active:hover .list-group-item-heading > .small,
.list-group-item.active:focus .list-group-item-heading > .small {
  color: inherit;
}
.list-group-item.active .list-group-item-text,
.list-group-item.active:hover .list-group-item-text,
.list-group-item.active:focus .list-group-item-text {
  color: #c7ddef;
}
.list-group-item-success {
  color: #3c763d;
  background-color: #dff0d8;
}
a.list-group-item-success,
button.list-group-item-success {
  color: #3c763d;
}
a.list-group-item-success .list-group-item-heading,
button.list-group-item-success .list-group-item-heading {
  color: inherit;
}
a.list-group-item-success:hover,
button.list-group-item-success:hover,
a.list-group-item-success:focus,
button.list-group-item-success:focus {
  color: #3c763d;
  background-color: #d0e9c6;
}
a.list-group-item-success.active,
button.list-group-item-success.active,
a.list-group-item-success.active:hover,
button.list-group-item-success.active:hover,
a.list-group-item-success.active:focus,
button.list-group-item-success.active:focus {
  color: #fff;
  background-color: #3c763d;
  border-color: #3c763d;
}
.list-group-item-info {
  color: #31708f;
  background-color: #d9edf7;
}
a.list-group-item-info,
button.list-group-item-info {
  color: #31708f;
}
a.list-group-item-info .list-group-item-heading,
button.list-group-item-info .list-group-item-heading {
  color: inherit;
}
a.list-group-item-info:hover,
button.list-group-item-info:hover,
a.list-group-item-info:focus,
button.list-group-item-info:focus {
  color: #31708f;
  background-color: #c4e3f3;
}
a.list-group-item-info.active,
button.list-group-item-info.active,
a.list-group-item-info.active:hover,
button.list-group-item-info.active:hover,
a.list-group-item-info.active:focus,
button.list-group-item-info.active:focus {
  color: #fff;
  background-color: #31708f;
  border-color: #31708f;
}
.list-group-item-warning {
  color: #8a6d3b;
  background-color: #fcf8e3;
}
a.list-group-item-warning,
button.list-group-item-warning {
  color: #8a6d3b;
}
a.list-group-item-warning .list-group-item-heading,
button.list-group-item-warning .list-group-item-heading {
  color: inherit;
}
a.list-group-item-warning:hover,
button.list-group-item-warning:hover,
a.list-group-item-warning:focus,
button.list-group-item-warning:focus {
  color: #8a6d3b;
  background-color: #faf2cc;
}
a.list-group-item-warning.active,
button.list-group-item-warning.active,
a.list-group-item-warning.active:hover,
button.list-group-item-warning.active:hover,
a.list-group-item-warning.active:focus,
button.list-group-item-warning.active:focus {
  color: #fff;
  background-color: #8a6d3b;
  border-color: #8a6d3b;
}
.list-group-item-danger {
  color: #a94442;
  background-color: #f2dede;
}
a.list-group-item-danger,
button.list-group-item-danger {
  color: #a94442;
}
a.list-group-item-danger .list-group-item-heading,
button.list-group-item-danger .list-group-item-heading {
  color: inherit;
}
a.list-group-item-danger:hover,
button.list-group-item-danger:hover,
a.list-group-item-danger:focus,
button.list-group-item-danger:focus {
  color: #a94442;
  background-color: #ebcccc;
}
a.list-group-item-danger.active,
button.list-group-item-danger.active,
a.list-group-item-danger.active:hover,
button.list-group-item-danger.active:hover,
a.list-group-item-danger.active:focus,
button.list-group-item-danger.active:focus {
  color: #fff;
  background-color: #a94442;
  border-color: #a94442;
}
.list-group-item-heading {
  margin-top: 0;
  margin-bottom: 5px;
}
.list-group-item-text {
  margin-bottom: 0;
  line-height: 1.3;
}
.panel {
  margin-bottom: 18px;
  background-color: #fff;
  border: 1px solid transparent;
  border-radius: 2px;
  -webkit-box-shadow: 0 1px 1px rgba(0, 0, 0, 0.05);
  box-shadow: 0 1px 1px rgba(0, 0, 0, 0.05);
}
.panel-body {
  padding: 15px;
}
.panel-heading {
  padding: 10px 15px;
  border-bottom: 1px solid transparent;
  border-top-right-radius: 1px;
  border-top-left-radius: 1px;
}
.panel-heading > .dropdown .dropdown-toggle {
  color: inherit;
}
.panel-title {
  margin-top: 0;
  margin-bottom: 0;
  font-size: 15px;
  color: inherit;
}
.panel-title > a,
.panel-title > small,
.panel-title > .small,
.panel-title > small > a,
.panel-title > .small > a {
  color: inherit;
}
.panel-footer {
  padding: 10px 15px;
  background-color: #f5f5f5;
  border-top: 1px solid #ddd;
  border-bottom-right-radius: 1px;
  border-bottom-left-radius: 1px;
}
.panel > .list-group,
.panel > .panel-collapse > .list-group {
  margin-bottom: 0;
}
.panel > .list-group .list-group-item,
.panel > .panel-collapse > .list-group .list-group-item {
  border-width: 1px 0;
  border-radius: 0;
}
.panel > .list-group:first-child .list-group-item:first-child,
.panel > .panel-collapse > .list-group:first-child .list-group-item:first-child {
  border-top: 0;
  border-top-right-radius: 1px;
  border-top-left-radius: 1px;
}
.panel > .list-group:last-child .list-group-item:last-child,
.panel > .panel-collapse > .list-group:last-child .list-group-item:last-child {
  border-bottom: 0;
  border-bottom-right-radius: 1px;
  border-bottom-left-radius: 1px;
}
.panel > .panel-heading + .panel-collapse > .list-group .list-group-item:first-child {
  border-top-right-radius: 0;
  border-top-left-radius: 0;
}
.panel-heading + .list-group .list-group-item:first-child {
  border-top-width: 0;
}
.list-group + .panel-footer {
  border-top-width: 0;
}
.panel > .table,
.panel > .table-responsive > .table,
.panel > .panel-collapse > .table {
  margin-bottom: 0;
}
.panel > .table caption,
.panel > .table-responsive > .table caption,
.panel > .panel-collapse > .table caption {
  padding-left: 15px;
  padding-right: 15px;
}
.panel > .table:first-child,
.panel > .table-responsive:first-child > .table:first-child {
  border-top-right-radius: 1px;
  border-top-left-radius: 1px;
}
.panel > .table:first-child > thead:first-child > tr:first-child,
.panel > .table-responsive:first-child > .table:first-child > thead:first-child > tr:first-child,
.panel > .table:first-child > tbody:first-child > tr:first-child,
.panel > .table-responsive:first-child > .table:first-child > tbody:first-child > tr:first-child {
  border-top-left-radius: 1px;
  border-top-right-radius: 1px;
}
.panel > .table:first-child > thead:first-child > tr:first-child td:first-child,
.panel > .table-responsive:first-child > .table:first-child > thead:first-child > tr:first-child td:first-child,
.panel > .table:first-child > tbody:first-child > tr:first-child td:first-child,
.panel > .table-responsive:first-child > .table:first-child > tbody:first-child > tr:first-child td:first-child,
.panel > .table:first-child > thead:first-child > tr:first-child th:first-child,
.panel > .table-responsive:first-child > .table:first-child > thead:first-child > tr:first-child th:first-child,
.panel > .table:first-child > tbody:first-child > tr:first-child th:first-child,
.panel > .table-responsive:first-child > .table:first-child > tbody:first-child > tr:first-child th:first-child {
  border-top-left-radius: 1px;
}
.panel > .table:first-child > thead:first-child > tr:first-child td:last-child,
.panel > .table-responsive:first-child > .table:first-child > thead:first-child > tr:first-child td:last-child,
.panel > .table:first-child > tbody:first-child > tr:first-child td:last-child,
.panel > .table-responsive:first-child > .table:first-child > tbody:first-child > tr:first-child td:last-child,
.panel > .table:first-child > thead:first-child > tr:first-child th:last-child,
.panel > .table-responsive:first-child > .table:first-child > thead:first-child > tr:first-child th:last-child,
.panel > .table:first-child > tbody:first-child > tr:first-child th:last-child,
.panel > .table-responsive:first-child > .table:first-child > tbody:first-child > tr:first-child th:last-child {
  border-top-right-radius: 1px;
}
.panel > .table:last-child,
.panel > .table-responsive:last-child > .table:last-child {
  border-bottom-right-radius: 1px;
  border-bottom-left-radius: 1px;
}
.panel > .table:last-child > tbody:last-child > tr:last-child,
.panel > .table-responsive:last-child > .table:last-child > tbody:last-child > tr:last-child,
.panel > .table:last-child > tfoot:last-child > tr:last-child,
.panel > .table-responsive:last-child > .table:last-child > tfoot:last-child > tr:last-child {
  border-bottom-left-radius: 1px;
  border-bottom-right-radius: 1px;
}
.panel > .table:last-child > tbody:last-child > tr:last-child td:first-child,
.panel > .table-responsive:last-child > .table:last-child > tbody:last-child > tr:last-child td:first-child,
.panel > .table:last-child > tfoot:last-child > tr:last-child td:first-child,
.panel > .table-responsive:last-child > .table:last-child > tfoot:last-child > tr:last-child td:first-child,
.panel > .table:last-child > tbody:last-child > tr:last-child th:first-child,
.panel > .table-responsive:last-child > .table:last-child > tbody:last-child > tr:last-child th:first-child,
.panel > .table:last-child > tfoot:last-child > tr:last-child th:first-child,
.panel > .table-responsive:last-child > .table:last-child > tfoot:last-child > tr:last-child th:first-child {
  border-bottom-left-radius: 1px;
}
.panel > .table:last-child > tbody:last-child > tr:last-child td:last-child,
.panel > .table-responsive:last-child > .table:last-child > tbody:last-child > tr:last-child td:last-child,
.panel > .table:last-child > tfoot:last-child > tr:last-child td:last-child,
.panel > .table-responsive:last-child > .table:last-child > tfoot:last-child > tr:last-child td:last-child,
.panel > .table:last-child > tbody:last-child > tr:last-child th:last-child,
.panel > .table-responsive:last-child > .table:last-child > tbody:last-child > tr:last-child th:last-child,
.panel > .table:last-child > tfoot:last-child > tr:last-child th:last-child,
.panel > .table-responsive:last-child > .table:last-child > tfoot:last-child > tr:last-child th:last-child {
  border-bottom-right-radius: 1px;
}
.panel > .panel-body + .table,
.panel > .panel-body + .table-responsive,
.panel > .table + .panel-body,
.panel > .table-responsive + .panel-body {
  border-top: 1px solid #ddd;
}
.panel > .table > tbody:first-child > tr:first-child th,
.panel > .table > tbody:first-child > tr:first-child td {
  border-top: 0;
}
.panel > .table-bordered,
.panel > .table-responsive > .table-bordered {
  border: 0;
}
.panel > .table-bordered > thead > tr > th:first-child,
.panel > .table-responsive > .table-bordered > thead > tr > th:first-child,
.panel > .table-bordered > tbody > tr > th:first-child,
.panel > .table-responsive > .table-bordered > tbody > tr > th:first-child,
.panel > .table-bordered > tfoot > tr > th:first-child,
.panel > .table-responsive > .table-bordered > tfoot > tr > th:first-child,
.panel > .table-bordered > thead > tr > td:first-child,
.panel > .table-responsive > .table-bordered > thead > tr > td:first-child,
.panel > .table-bordered > tbody > tr > td:first-child,
.panel > .table-responsive > .table-bordered > tbody > tr > td:first-child,
.panel > .table-bordered > tfoot > tr > td:first-child,
.panel > .table-responsive > .table-bordered > tfoot > tr > td:first-child {
  border-left: 0;
}
.panel > .table-bordered > thead > tr > th:last-child,
.panel > .table-responsive > .table-bordered > thead > tr > th:last-child,
.panel > .table-bordered > tbody > tr > th:last-child,
.panel > .table-responsive > .table-bordered > tbody > tr > th:last-child,
.panel > .table-bordered > tfoot > tr > th:last-child,
.panel > .table-responsive > .table-bordered > tfoot > tr > th:last-child,
.panel > .table-bordered > thead > tr > td:last-child,
.panel > .table-responsive > .table-bordered > thead > tr > td:last-child,
.panel > .table-bordered > tbody > tr > td:last-child,
.panel > .table-responsive > .table-bordered > tbody > tr > td:last-child,
.panel > .table-bordered > tfoot > tr > td:last-child,
.panel > .table-responsive > .table-bordered > tfoot > tr > td:last-child {
  border-right: 0;
}
.panel > .table-bordered > thead > tr:first-child > td,
.panel > .table-responsive > .table-bordered > thead > tr:first-child > td,
.panel > .table-bordered > tbody > tr:first-child > td,
.panel > .table-responsive > .table-bordered > tbody > tr:first-child > td,
.panel > .table-bordered > thead > tr:first-child > th,
.panel > .table-responsive > .table-bordered > thead > tr:first-child > th,
.panel > .table-bordered > tbody > tr:first-child > th,
.panel > .table-responsive > .table-bordered > tbody > tr:first-child > th {
  border-bottom: 0;
}
.panel > .table-bordered > tbody > tr:last-child > td,
.panel > .table-responsive > .table-bordered > tbody > tr:last-child > td,
.panel > .table-bordered > tfoot > tr:last-child > td,
.panel > .table-responsive > .table-bordered > tfoot > tr:last-child > td,
.panel > .table-bordered > tbody > tr:last-child > th,
.panel > .table-responsive > .table-bordered > tbody > tr:last-child > th,
.panel > .table-bordered > tfoot > tr:last-child > th,
.panel > .table-responsive > .table-bordered > tfoot > tr:last-child > th {
  border-bottom: 0;
}
.panel > .table-responsive {
  border: 0;
  margin-bottom: 0;
}
.panel-group {
  margin-bottom: 18px;
}
.panel-group .panel {
  margin-bottom: 0;
  border-radius: 2px;
}
.panel-group .panel + .panel {
  margin-top: 5px;
}
.panel-group .panel-heading {
  border-bottom: 0;
}
.panel-group .panel-heading + .panel-collapse > .panel-body,
.panel-group .panel-heading + .panel-collapse > .list-group {
  border-top: 1px solid #ddd;
}
.panel-group .panel-footer {
  border-top: 0;
}
.panel-group .panel-footer + .panel-collapse .panel-body {
  border-bottom: 1px solid #ddd;
}
.panel-default {
  border-color: #ddd;
}
.panel-default > .panel-heading {
  color: #333333;
  background-color: #f5f5f5;
  border-color: #ddd;
}
.panel-default > .panel-heading + .panel-collapse > .panel-body {
  border-top-color: #ddd;
}
.panel-default > .panel-heading .badge {
  color: #f5f5f5;
  background-color: #333333;
}
.panel-default > .panel-footer + .panel-collapse > .panel-body {
  border-bottom-color: #ddd;
}
.panel-primary {
  border-color: #337ab7;
}
.panel-primary > .panel-heading {
  color: #fff;
  background-color: #337ab7;
  border-color: #337ab7;
}
.panel-primary > .panel-heading + .panel-collapse > .panel-body {
  border-top-color: #337ab7;
}
.panel-primary > .panel-heading .badge {
  color: #337ab7;
  background-color: #fff;
}
.panel-primary > .panel-footer + .panel-collapse > .panel-body {
  border-bottom-color: #337ab7;
}
.panel-success {
  border-color: #d6e9c6;
}
.panel-success > .panel-heading {
  color: #3c763d;
  background-color: #dff0d8;
  border-color: #d6e9c6;
}
.panel-success > .panel-heading + .panel-collapse > .panel-body {
  border-top-color: #d6e9c6;
}
.panel-success > .panel-heading .badge {
  color: #dff0d8;
  background-color: #3c763d;
}
.panel-success > .panel-footer + .panel-collapse > .panel-body {
  border-bottom-color: #d6e9c6;
}
.panel-info {
  border-color: #bce8f1;
}
.panel-info > .panel-heading {
  color: #31708f;
  background-color: #d9edf7;
  border-color: #bce8f1;
}
.panel-info > .panel-heading + .panel-collapse > .panel-body {
  border-top-color: #bce8f1;
}
.panel-info > .panel-heading .badge {
  color: #d9edf7;
  background-color: #31708f;
}
.panel-info > .panel-footer + .panel-collapse > .panel-body {
  border-bottom-color: #bce8f1;
}
.panel-warning {
  border-color: #faebcc;
}
.panel-warning > .panel-heading {
  color: #8a6d3b;
  background-color: #fcf8e3;
  border-color: #faebcc;
}
.panel-warning > .panel-heading + .panel-collapse > .panel-body {
  border-top-color: #faebcc;
}
.panel-warning > .panel-heading .badge {
  color: #fcf8e3;
  background-color: #8a6d3b;
}
.panel-warning > .panel-footer + .panel-collapse > .panel-body {
  border-bottom-color: #faebcc;
}
.panel-danger {
  border-color: #ebccd1;
}
.panel-danger > .panel-heading {
  color: #a94442;
  background-color: #f2dede;
  border-color: #ebccd1;
}
.panel-danger > .panel-heading + .panel-collapse > .panel-body {
  border-top-color: #ebccd1;
}
.panel-danger > .panel-heading .badge {
  color: #f2dede;
  background-color: #a94442;
}
.panel-danger > .panel-footer + .panel-collapse > .panel-body {
  border-bottom-color: #ebccd1;
}
.embed-responsive {
  position: relative;
  display: block;
  height: 0;
  padding: 0;
  overflow: hidden;
}
.embed-responsive .embed-responsive-item,
.embed-responsive iframe,
.embed-responsive embed,
.embed-responsive object,
.embed-responsive video {
  position: absolute;
  top: 0;
  left: 0;
  bottom: 0;
  height: 100%;
  width: 100%;
  border: 0;
}
.embed-responsive-16by9 {
  padding-bottom: 56.25%;
}
.embed-responsive-4by3 {
  padding-bottom: 75%;
}
.well {
  min-height: 20px;
  padding: 19px;
  margin-bottom: 20px;
  background-color: #f5f5f5;
  border: 1px solid #e3e3e3;
  border-radius: 2px;
  -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.05);
  box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.05);
}
.well blockquote {
  border-color: #ddd;
  border-color: rgba(0, 0, 0, 0.15);
}
.well-lg {
  padding: 24px;
  border-radius: 3px;
}
.well-sm {
  padding: 9px;
  border-radius: 1px;
}
.close {
  float: right;
  font-size: 19.5px;
  font-weight: bold;
  line-height: 1;
  color: #000;
  text-shadow: 0 1px 0 #fff;
  opacity: 0.2;
  filter: alpha(opacity=20);
}
.close:hover,
.close:focus {
  color: #000;
  text-decoration: none;
  cursor: pointer;
  opacity: 0.5;
  filter: alpha(opacity=50);
}
button.close {
  padding: 0;
  cursor: pointer;
  background: transparent;
  border: 0;
  -webkit-appearance: none;
}
.modal-open {
  overflow: hidden;
}
.modal {
  display: none;
  overflow: hidden;
  position: fixed;
  top: 0;
  right: 0;
  bottom: 0;
  left: 0;
  z-index: 1050;
  -webkit-overflow-scrolling: touch;
  outline: 0;
}
.modal.fade .modal-dialog {
  -webkit-transform: translate(0, -25%);
  -ms-transform: translate(0, -25%);
  -o-transform: translate(0, -25%);
  transform: translate(0, -25%);
  -webkit-transition: -webkit-transform 0.3s ease-out;
  -moz-transition: -moz-transform 0.3s ease-out;
  -o-transition: -o-transform 0.3s ease-out;
  transition: transform 0.3s ease-out;
}
.modal.in .modal-dialog {
  -webkit-transform: translate(0, 0);
  -ms-transform: translate(0, 0);
  -o-transform: translate(0, 0);
  transform: translate(0, 0);
}
.modal-open .modal {
  overflow-x: hidden;
  overflow-y: auto;
}
.modal-dialog {
  position: relative;
  width: auto;
  margin: 10px;
}
.modal-content {
  position: relative;
  background-color: #fff;
  border: 1px solid #999;
  border: 1px solid rgba(0, 0, 0, 0.2);
  border-radius: 3px;
  -webkit-box-shadow: 0 3px 9px rgba(0, 0, 0, 0.5);
  box-shadow: 0 3px 9px rgba(0, 0, 0, 0.5);
  background-clip: padding-box;
  outline: 0;
}
.modal-backdrop {
  position: fixed;
  top: 0;
  right: 0;
  bottom: 0;
  left: 0;
  z-index: 1040;
  background-color: #000;
}
.modal-backdrop.fade {
  opacity: 0;
  filter: alpha(opacity=0);
}
.modal-backdrop.in {
  opacity: 0.5;
  filter: alpha(opacity=50);
}
.modal-header {
  padding: 15px;
  border-bottom: 1px solid #e5e5e5;
}
.modal-header .close {
  margin-top: -2px;
}
.modal-title {
  margin: 0;
  line-height: 1.42857143;
}
.modal-body {
  position: relative;
  padding: 15px;
}
.modal-footer {
  padding: 15px;
  text-align: right;
  border-top: 1px solid #e5e5e5;
}
.modal-footer .btn + .btn {
  margin-left: 5px;
  margin-bottom: 0;
}
.modal-footer .btn-group .btn + .btn {
  margin-left: -1px;
}
.modal-footer .btn-block + .btn-block {
  margin-left: 0;
}
.modal-scrollbar-measure {
  position: absolute;
  top: -9999px;
  width: 50px;
  height: 50px;
  overflow: scroll;
}
@media (min-width: 768px) {
  .modal-dialog {
    width: 600px;
    margin: 30px auto;
  }
  .modal-content {
    -webkit-box-shadow: 0 5px 15px rgba(0, 0, 0, 0.5);
    box-shadow: 0 5px 15px rgba(0, 0, 0, 0.5);
  }
  .modal-sm {
    width: 300px;
  }
}
@media (min-width: 992px) {
  .modal-lg {
    width: 900px;
  }
}
.tooltip {
  position: absolute;
  z-index: 1070;
  display: block;
  font-family: "Helvetica Neue", Helvetica, Arial, sans-serif;
  font-style: normal;
  font-weight: normal;
  letter-spacing: normal;
  line-break: auto;
  line-height: 1.42857143;
  text-align: left;
  text-align: start;
  text-decoration: none;
  text-shadow: none;
  text-transform: none;
  white-space: normal;
  word-break: normal;
  word-spacing: normal;
  word-wrap: normal;
  font-size: 12px;
  opacity: 0;
  filter: alpha(opacity=0);
}
.tooltip.in {
  opacity: 0.9;
  filter: alpha(opacity=90);
}
.tooltip.top {
  margin-top: -3px;
  padding: 5px 0;
}
.tooltip.right {
  margin-left: 3px;
  padding: 0 5px;
}
.tooltip.bottom {
  margin-top: 3px;
  padding: 5px 0;
}
.tooltip.left {
  margin-left: -3px;
  padding: 0 5px;
}
.tooltip-inner {
  max-width: 200px;
  padding: 3px 8px;
  color: #fff;
  text-align: center;
  background-color: #000;
  border-radius: 2px;
}
.tooltip-arrow {
  position: absolute;
  width: 0;
  height: 0;
  border-color: transparent;
  border-style: solid;
}
.tooltip.top .tooltip-arrow {
  bottom: 0;
  left: 50%;
  margin-left: -5px;
  border-width: 5px 5px 0;
  border-top-color: #000;
}
.tooltip.top-left .tooltip-arrow {
  bottom: 0;
  right: 5px;
  margin-bottom: -5px;
  border-width: 5px 5px 0;
  border-top-color: #000;
}
.tooltip.top-right .tooltip-arrow {
  bottom: 0;
  left: 5px;
  margin-bottom: -5px;
  border-width: 5px 5px 0;
  border-top-color: #000;
}
.tooltip.right .tooltip-arrow {
  top: 50%;
  left: 0;
  margin-top: -5px;
  border-width: 5px 5px 5px 0;
  border-right-color: #000;
}
.tooltip.left .tooltip-arrow {
  top: 50%;
  right: 0;
  margin-top: -5px;
  border-width: 5px 0 5px 5px;
  border-left-color: #000;
}
.tooltip.bottom .tooltip-arrow {
  top: 0;
  left: 50%;
  margin-left: -5px;
  border-width: 0 5px 5px;
  border-bottom-color: #000;
}
.tooltip.bottom-left .tooltip-arrow {
  top: 0;
  right: 5px;
  margin-top: -5px;
  border-width: 0 5px 5px;
  border-bottom-color: #000;
}
.tooltip.bottom-right .tooltip-arrow {
  top: 0;
  left: 5px;
  margin-top: -5px;
  border-width: 0 5px 5px;
  border-bottom-color: #000;
}
.popover {
  position: absolute;
  top: 0;
  left: 0;
  z-index: 1060;
  display: none;
  max-width: 276px;
  padding: 1px;
  font-family: "Helvetica Neue", Helvetica, Arial, sans-serif;
  font-style: normal;
  font-weight: normal;
  letter-spacing: normal;
  line-break: auto;
  line-height: 1.42857143;
  text-align: left;
  text-align: start;
  text-decoration: none;
  text-shadow: none;
  text-transform: none;
  white-space: normal;
  word-break: normal;
  word-spacing: normal;
  word-wrap: normal;
  font-size: 13px;
  background-color: #fff;
  background-clip: padding-box;
  border: 1px solid #ccc;
  border: 1px solid rgba(0, 0, 0, 0.2);
  border-radius: 3px;
  -webkit-box-shadow: 0 5px 10px rgba(0, 0, 0, 0.2);
  box-shadow: 0 5px 10px rgba(0, 0, 0, 0.2);
}
.popover.top {
  margin-top: -10px;
}
.popover.right {
  margin-left: 10px;
}
.popover.bottom {
  margin-top: 10px;
}
.popover.left {
  margin-left: -10px;
}
.popover-title {
  margin: 0;
  padding: 8px 14px;
  font-size: 13px;
  background-color: #f7f7f7;
  border-bottom: 1px solid #ebebeb;
  border-radius: 2px 2px 0 0;
}
.popover-content {
  padding: 9px 14px;
}
.popover > .arrow,
.popover > .arrow:after {
  position: absolute;
  display: block;
  width: 0;
  height: 0;
  border-color: transparent;
  border-style: solid;
}
.popover > .arrow {
  border-width: 11px;
}
.popover > .arrow:after {
  border-width: 10px;
  content: "";
}
.popover.top > .arrow {
  left: 50%;
  margin-left: -11px;
  border-bottom-width: 0;
  border-top-color: #999999;
  border-top-color: rgba(0, 0, 0, 0.25);
  bottom: -11px;
}
.popover.top > .arrow:after {
  content: " ";
  bottom: 1px;
  margin-left: -10px;
  border-bottom-width: 0;
  border-top-color: #fff;
}
.popover.right > .arrow {
  top: 50%;
  left: -11px;
  margin-top: -11px;
  border-left-width: 0;
  border-right-color: #999999;
  border-right-color: rgba(0, 0, 0, 0.25);
}
.popover.right > .arrow:after {
  content: " ";
  left: 1px;
  bottom: -10px;
  border-left-width: 0;
  border-right-color: #fff;
}
.popover.bottom > .arrow {
  left: 50%;
  margin-left: -11px;
  border-top-width: 0;
  border-bottom-color: #999999;
  border-bottom-color: rgba(0, 0, 0, 0.25);
  top: -11px;
}
.popover.bottom > .arrow:after {
  content: " ";
  top: 1px;
  margin-left: -10px;
  border-top-width: 0;
  border-bottom-color: #fff;
}
.popover.left > .arrow {
  top: 50%;
  right: -11px;
  margin-top: -11px;
  border-right-width: 0;
  border-left-color: #999999;
  border-left-color: rgba(0, 0, 0, 0.25);
}
.popover.left > .arrow:after {
  content: " ";
  right: 1px;
  border-right-width: 0;
  border-left-color: #fff;
  bottom: -10px;
}
.carousel {
  position: relative;
}
.carousel-inner {
  position: relative;
  overflow: hidden;
  width: 100%;
}
.carousel-inner > .item {
  display: none;
  position: relative;
  -webkit-transition: 0.6s ease-in-out left;
  -o-transition: 0.6s ease-in-out left;
  transition: 0.6s ease-in-out left;
}
.carousel-inner > .item > img,
.carousel-inner > .item > a > img {
  line-height: 1;
}
@media all and (transform-3d), (-webkit-transform-3d) {
  .carousel-inner > .item {
    -webkit-transition: -webkit-transform 0.6s ease-in-out;
    -moz-transition: -moz-transform 0.6s ease-in-out;
    -o-transition: -o-transform 0.6s ease-in-out;
    transition: transform 0.6s ease-in-out;
    -webkit-backface-visibility: hidden;
    -moz-backface-visibility: hidden;
    backface-visibility: hidden;
    -webkit-perspective: 1000px;
    -moz-perspective: 1000px;
    perspective: 1000px;
  }
  .carousel-inner > .item.next,
  .carousel-inner > .item.active.right {
    -webkit-transform: translate3d(100%, 0, 0);
    transform: translate3d(100%, 0, 0);
    left: 0;
  }
  .carousel-inner > .item.prev,
  .carousel-inner > .item.active.left {
    -webkit-transform: translate3d(-100%, 0, 0);
    transform: translate3d(-100%, 0, 0);
    left: 0;
  }
  .carousel-inner > .item.next.left,
  .carousel-inner > .item.prev.right,
  .carousel-inner > .item.active {
    -webkit-transform: translate3d(0, 0, 0);
    transform: translate3d(0, 0, 0);
    left: 0;
  }
}
.carousel-inner > .active,
.carousel-inner > .next,
.carousel-inner > .prev {
  display: block;
}
.carousel-inner > .active {
  left: 0;
}
.carousel-inner > .next,
.carousel-inner > .prev {
  position: absolute;
  top: 0;
  width: 100%;
}
.carousel-inner > .next {
  left: 100%;
}
.carousel-inner > .prev {
  left: -100%;
}
.carousel-inner > .next.left,
.carousel-inner > .prev.right {
  left: 0;
}
.carousel-inner > .active.left {
  left: -100%;
}
.carousel-inner > .active.right {
  left: 100%;
}
.carousel-control {
  position: absolute;
  top: 0;
  left: 0;
  bottom: 0;
  width: 15%;
  opacity: 0.5;
  filter: alpha(opacity=50);
  font-size: 20px;
  color: #fff;
  text-align: center;
  text-shadow: 0 1px 2px rgba(0, 0, 0, 0.6);
  background-color: rgba(0, 0, 0, 0);
}
.carousel-control.left {
  background-image: -webkit-linear-gradient(left, rgba(0, 0, 0, 0.5) 0%, rgba(0, 0, 0, 0.0001) 100%);
  background-image: -o-linear-gradient(left, rgba(0, 0, 0, 0.5) 0%, rgba(0, 0, 0, 0.0001) 100%);
  background-image: linear-gradient(to right, rgba(0, 0, 0, 0.5) 0%, rgba(0, 0, 0, 0.0001) 100%);
  background-repeat: repeat-x;
  filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#80000000', endColorstr='#00000000', GradientType=1);
}
.carousel-control.right {
  left: auto;
  right: 0;
  background-image: -webkit-linear-gradient(left, rgba(0, 0, 0, 0.0001) 0%, rgba(0, 0, 0, 0.5) 100%);
  background-image: -o-linear-gradient(left, rgba(0, 0, 0, 0.0001) 0%, rgba(0, 0, 0, 0.5) 100%);
  background-image: linear-gradient(to right, rgba(0, 0, 0, 0.0001) 0%, rgba(0, 0, 0, 0.5) 100%);
  background-repeat: repeat-x;
  filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#00000000', endColorstr='#80000000', GradientType=1);
}
.carousel-control:hover,
.carousel-control:focus {
  outline: 0;
  color: #fff;
  text-decoration: none;
  opacity: 0.9;
  filter: alpha(opacity=90);
}
.carousel-control .icon-prev,
.carousel-control .icon-next,
.carousel-control .glyphicon-chevron-left,
.carousel-control .glyphicon-chevron-right {
  position: absolute;
  top: 50%;
  margin-top: -10px;
  z-index: 5;
  display: inline-block;
}
.carousel-control .icon-prev,
.carousel-control .glyphicon-chevron-left {
  left: 50%;
  margin-left: -10px;
}
.carousel-control .icon-next,
.carousel-control .glyphicon-chevron-right {
  right: 50%;
  margin-right: -10px;
}
.carousel-control .icon-prev,
.carousel-control .icon-next {
  width: 20px;
  height: 20px;
  line-height: 1;
  font-family: serif;
}
.carousel-control .icon-prev:before {
  content: '\2039';
}
.carousel-control .icon-next:before {
  content: '\203a';
}
.carousel-indicators {
  position: absolute;
  bottom: 10px;
  left: 50%;
  z-index: 15;
  width: 60%;
  margin-left: -30%;
  padding-left: 0;
  list-style: none;
  text-align: center;
}
.carousel-indicators li {
  display: inline-block;
  width: 10px;
  height: 10px;
  margin: 1px;
  text-indent: -999px;
  border: 1px solid #fff;
  border-radius: 10px;
  cursor: pointer;
  background-color: #000 \9;
  background-color: rgba(0, 0, 0, 0);
}
.carousel-indicators .active {
  margin: 0;
  width: 12px;
  height: 12px;
  background-color: #fff;
}
.carousel-caption {
  position: absolute;
  left: 15%;
  right: 15%;
  bottom: 20px;
  z-index: 10;
  padding-top: 20px;
  padding-bottom: 20px;
  color: #fff;
  text-align: center;
  text-shadow: 0 1px 2px rgba(0, 0, 0, 0.6);
}
.carousel-caption .btn {
  text-shadow: none;
}
@media screen and (min-width: 768px) {
  .carousel-control .glyphicon-chevron-left,
  .carousel-control .glyphicon-chevron-right,
  .carousel-control .icon-prev,
  .carousel-control .icon-next {
    width: 30px;
    height: 30px;
    margin-top: -10px;
    font-size: 30px;
  }
  .carousel-control .glyphicon-chevron-left,
  .carousel-control .icon-prev {
    margin-left: -10px;
  }
  .carousel-control .glyphicon-chevron-right,
  .carousel-control .icon-next {
    margin-right: -10px;
  }
  .carousel-caption {
    left: 20%;
    right: 20%;
    padding-bottom: 30px;
  }
  .carousel-indicators {
    bottom: 20px;
  }
}
.clearfix:before,
.clearfix:after,
.dl-horizontal dd:before,
.dl-horizontal dd:after,
.container:before,
.container:after,
.container-fluid:before,
.container-fluid:after,
.row:before,
.row:after,
.form-horizontal .form-group:before,
.form-horizontal .form-group:after,
.btn-toolbar:before,
.btn-toolbar:after,
.btn-group-vertical > .btn-group:before,
.btn-group-vertical > .btn-group:after,
.nav:before,
.nav:after,
.navbar:before,
.navbar:after,
.navbar-header:before,
.navbar-header:after,
.navbar-collapse:before,
.navbar-collapse:after,
.pager:before,
.pager:after,
.panel-body:before,
.panel-body:after,
.modal-header:before,
.modal-header:after,
.modal-footer:before,
.modal-footer:after,
.item_buttons:before,
.item_buttons:after {
  content: " ";
  display: table;
}
.clearfix:after,
.dl-horizontal dd:after,
.container:after,
.container-fluid:after,
.row:after,
.form-horizontal .form-group:after,
.btn-toolbar:after,
.btn-group-vertical > .btn-group:after,
.nav:after,
.navbar:after,
.navbar-header:after,
.navbar-collapse:after,
.pager:after,
.panel-body:after,
.modal-header:after,
.modal-footer:after,
.item_buttons:after {
  clear: both;
}
.center-block {
  display: block;
  margin-left: auto;
  margin-right: auto;
}
.pull-right {
  float: right !important;
}
.pull-left {
  float: left !important;
}
.hide {
  display: none !important;
}
.show {
  display: block !important;
}
.invisible {
  visibility: hidden;
}
.text-hide {
  font: 0/0 a;
  color: transparent;
  text-shadow: none;
  background-color: transparent;
  border: 0;
}
.hidden {
  display: none !important;
}
.affix {
  position: fixed;
}
@-ms-viewport {
  width: device-width;
}
.visible-xs,
.visible-sm,
.visible-md,
.visible-lg {
  display: none !important;
}
.visible-xs-block,
.visible-xs-inline,
.visible-xs-inline-block,
.visible-sm-block,
.visible-sm-inline,
.visible-sm-inline-block,
.visible-md-block,
.visible-md-inline,
.visible-md-inline-block,
.visible-lg-block,
.visible-lg-inline,
.visible-lg-inline-block {
  display: none !important;
}
@media (max-width: 767px) {
  .visible-xs {
    display: block !important;
  }
  table.visible-xs {
    display: table !important;
  }
  tr.visible-xs {
    display: table-row !important;
  }
  th.visible-xs,
  td.visible-xs {
    display: table-cell !important;
  }
}
@media (max-width: 767px) {
  .visible-xs-block {
    display: block !important;
  }
}
@media (max-width: 767px) {
  .visible-xs-inline {
    display: inline !important;
  }
}
@media (max-width: 767px) {
  .visible-xs-inline-block {
    display: inline-block !important;
  }
}
@media (min-width: 768px) and (max-width: 991px) {
  .visible-sm {
    display: block !important;
  }
  table.visible-sm {
    display: table !important;
  }
  tr.visible-sm {
    display: table-row !important;
  }
  th.visible-sm,
  td.visible-sm {
    display: table-cell !important;
  }
}
@media (min-width: 768px) and (max-width: 991px) {
  .visible-sm-block {
    display: block !important;
  }
}
@media (min-width: 768px) and (max-width: 991px) {
  .visible-sm-inline {
    display: inline !important;
  }
}
@media (min-width: 768px) and (max-width: 991px) {
  .visible-sm-inline-block {
    display: inline-block !important;
  }
}
@media (min-width: 992px) and (max-width: 1199px) {
  .visible-md {
    display: block !important;
  }
  table.visible-md {
    display: table !important;
  }
  tr.visible-md {
    display: table-row !important;
  }
  th.visible-md,
  td.visible-md {
    display: table-cell !important;
  }
}
@media (min-width: 992px) and (max-width: 1199px) {
  .visible-md-block {
    display: block !important;
  }
}
@media (min-width: 992px) and (max-width: 1199px) {
  .visible-md-inline {
    display: inline !important;
  }
}
@media (min-width: 992px) and (max-width: 1199px) {
  .visible-md-inline-block {
    display: inline-block !important;
  }
}
@media (min-width: 1200px) {
  .visible-lg {
    display: block !important;
  }
  table.visible-lg {
    display: table !important;
  }
  tr.visible-lg {
    display: table-row !important;
  }
  th.visible-lg,
  td.visible-lg {
    display: table-cell !important;
  }
}
@media (min-width: 1200px) {
  .visible-lg-block {
    display: block !important;
  }
}
@media (min-width: 1200px) {
  .visible-lg-inline {
    display: inline !important;
  }
}
@media (min-width: 1200px) {
  .visible-lg-inline-block {
    display: inline-block !important;
  }
}
@media (max-width: 767px) {
  .hidden-xs {
    display: none !important;
  }
}
@media (min-width: 768px) and (max-width: 991px) {
  .hidden-sm {
    display: none !important;
  }
}
@media (min-width: 992px) and (max-width: 1199px) {
  .hidden-md {
    display: none !important;
  }
}
@media (min-width: 1200px) {
  .hidden-lg {
    display: none !important;
  }
}
.visible-print {
  display: none !important;
}
@media print {
  .visible-print {
    display: block !important;
  }
  table.visible-print {
    display: table !important;
  }
  tr.visible-print {
    display: table-row !important;
  }
  th.visible-print,
  td.visible-print {
    display: table-cell !important;
  }
}
.visible-print-block {
  display: none !important;
}
@media print {
  .visible-print-block {
    display: block !important;
  }
}
.visible-print-inline {
  display: none !important;
}
@media print {
  .visible-print-inline {
    display: inline !important;
  }
}
.visible-print-inline-block {
  display: none !important;
}
@media print {
  .visible-print-inline-block {
    display: inline-block !important;
  }
}
@media print {
  .hidden-print {
    display: none !important;
  }
}
/*!
*
* Font Awesome
*
*/
/*!
 *  Font Awesome 4.7.0 by @davegandy - http://fontawesome.io - @fontawesome
 *  License - http://fontawesome.io/license (Font: SIL OFL 1.1, CSS: MIT License)
 */
/* FONT PATH
 * -------------------------- */
@font-face {
  font-family: 'FontAwesome';
  src: url('../components/font-awesome/fonts/fontawesome-webfont.eot?v=4.7.0');
  src: url('../components/font-awesome/fonts/fontawesome-webfont.eot?#iefix&v=4.7.0') format('embedded-opentype'), url('../components/font-awesome/fonts/fontawesome-webfont.woff2?v=4.7.0') format('woff2'), url('../components/font-awesome/fonts/fontawesome-webfont.woff?v=4.7.0') format('woff'), url('../components/font-awesome/fonts/fontawesome-webfont.ttf?v=4.7.0') format('truetype'), url('../components/font-awesome/fonts/fontawesome-webfont.svg?v=4.7.0#fontawesomeregular') format('svg');
  font-weight: normal;
  font-style: normal;
}
.fa {
  display: inline-block;
  font: normal normal normal 14px/1 FontAwesome;
  font-size: inherit;
  text-rendering: auto;
  -webkit-font-smoothing: antialiased;
  -moz-osx-font-smoothing: grayscale;
}
/* makes the font 33% larger relative to the icon container */
.fa-lg {
  font-size: 1.33333333em;
  line-height: 0.75em;
  vertical-align: -15%;
}
.fa-2x {
  font-size: 2em;
}
.fa-3x {
  font-size: 3em;
}
.fa-4x {
  font-size: 4em;
}
.fa-5x {
  font-size: 5em;
}
.fa-fw {
  width: 1.28571429em;
  text-align: center;
}
.fa-ul {
  padding-left: 0;
  margin-left: 2.14285714em;
  list-style-type: none;
}
.fa-ul > li {
  position: relative;
}
.fa-li {
  position: absolute;
  left: -2.14285714em;
  width: 2.14285714em;
  top: 0.14285714em;
  text-align: center;
}
.fa-li.fa-lg {
  left: -1.85714286em;
}
.fa-border {
  padding: .2em .25em .15em;
  border: solid 0.08em #eee;
  border-radius: .1em;
}
.fa-pull-left {
  float: left;
}
.fa-pull-right {
  float: right;
}
.fa.fa-pull-left {
  margin-right: .3em;
}
.fa.fa-pull-right {
  margin-left: .3em;
}
/* Deprecated as of 4.4.0 */
.pull-right {
  float: right;
}
.pull-left {
  float: left;
}
.fa.pull-left {
  margin-right: .3em;
}
.fa.pull-right {
  margin-left: .3em;
}
.fa-spin {
  -webkit-animation: fa-spin 2s infinite linear;
  animation: fa-spin 2s infinite linear;
}
.fa-pulse {
  -webkit-animation: fa-spin 1s infinite steps(8);
  animation: fa-spin 1s infinite steps(8);
}
@-webkit-keyframes fa-spin {
  0% {
    -webkit-transform: rotate(0deg);
    transform: rotate(0deg);
  }
  100% {
    -webkit-transform: rotate(359deg);
    transform: rotate(359deg);
  }
}
@keyframes fa-spin {
  0% {
    -webkit-transform: rotate(0deg);
    transform: rotate(0deg);
  }
  100% {
    -webkit-transform: rotate(359deg);
    transform: rotate(359deg);
  }
}
.fa-rotate-90 {
  -ms-filter: "progid:DXImageTransform.Microsoft.BasicImage(rotation=1)";
  -webkit-transform: rotate(90deg);
  -ms-transform: rotate(90deg);
  transform: rotate(90deg);
}
.fa-rotate-180 {
  -ms-filter: "progid:DXImageTransform.Microsoft.BasicImage(rotation=2)";
  -webkit-transform: rotate(180deg);
  -ms-transform: rotate(180deg);
  transform: rotate(180deg);
}
.fa-rotate-270 {
  -ms-filter: "progid:DXImageTransform.Microsoft.BasicImage(rotation=3)";
  -webkit-transform: rotate(270deg);
  -ms-transform: rotate(270deg);
  transform: rotate(270deg);
}
.fa-flip-horizontal {
  -ms-filter: "progid:DXImageTransform.Microsoft.BasicImage(rotation=0, mirror=1)";
  -webkit-transform: scale(-1, 1);
  -ms-transform: scale(-1, 1);
  transform: scale(-1, 1);
}
.fa-flip-vertical {
  -ms-filter: "progid:DXImageTransform.Microsoft.BasicImage(rotation=2, mirror=1)";
  -webkit-transform: scale(1, -1);
  -ms-transform: scale(1, -1);
  transform: scale(1, -1);
}
:root .fa-rotate-90,
:root .fa-rotate-180,
:root .fa-rotate-270,
:root .fa-flip-horizontal,
:root .fa-flip-vertical {
  filter: none;
}
.fa-stack {
  position: relative;
  display: inline-block;
  width: 2em;
  height: 2em;
  line-height: 2em;
  vertical-align: middle;
}
.fa-stack-1x,
.fa-stack-2x {
  position: absolute;
  left: 0;
  width: 100%;
  text-align: center;
}
.fa-stack-1x {
  line-height: inherit;
}
.fa-stack-2x {
  font-size: 2em;
}
.fa-inverse {
  color: #fff;
}
/* Font Awesome uses the Unicode Private Use Area (PUA) to ensure screen
   readers do not read off random characters that represent icons */
.fa-glass:before {
  content: "\f000";
}
.fa-music:before {
  content: "\f001";
}
.fa-search:before {
  content: "\f002";
}
.fa-envelope-o:before {
  content: "\f003";
}
.fa-heart:before {
  content: "\f004";
}
.fa-star:before {
  content: "\f005";
}
.fa-star-o:before {
  content: "\f006";
}
.fa-user:before {
  content: "\f007";
}
.fa-film:before {
  content: "\f008";
}
.fa-th-large:before {
  content: "\f009";
}
.fa-th:before {
  content: "\f00a";
}
.fa-th-list:before {
  content: "\f00b";
}
.fa-check:before {
  content: "\f00c";
}
.fa-remove:before,
.fa-close:before,
.fa-times:before {
  content: "\f00d";
}
.fa-search-plus:before {
  content: "\f00e";
}
.fa-search-minus:before {
  content: "\f010";
}
.fa-power-off:before {
  content: "\f011";
}
.fa-signal:before {
  content: "\f012";
}
.fa-gear:before,
.fa-cog:before {
  content: "\f013";
}
.fa-trash-o:before {
  content: "\f014";
}
.fa-home:before {
  content: "\f015";
}
.fa-file-o:before {
  content: "\f016";
}
.fa-clock-o:before {
  content: "\f017";
}
.fa-road:before {
  content: "\f018";
}
.fa-download:before {
  content: "\f019";
}
.fa-arrow-circle-o-down:before {
  content: "\f01a";
}
.fa-arrow-circle-o-up:before {
  content: "\f01b";
}
.fa-inbox:before {
  content: "\f01c";
}
.fa-play-circle-o:before {
  content: "\f01d";
}
.fa-rotate-right:before,
.fa-repeat:before {
  content: "\f01e";
}
.fa-refresh:before {
  content: "\f021";
}
.fa-list-alt:before {
  content: "\f022";
}
.fa-lock:before {
  content: "\f023";
}
.fa-flag:before {
  content: "\f024";
}
.fa-headphones:before {
  content: "\f025";
}
.fa-volume-off:before {
  content: "\f026";
}
.fa-volume-down:before {
  content: "\f027";
}
.fa-volume-up:before {
  content: "\f028";
}
.fa-qrcode:before {
  content: "\f029";
}
.fa-barcode:before {
  content: "\f02a";
}
.fa-tag:before {
  content: "\f02b";
}
.fa-tags:before {
  content: "\f02c";
}
.fa-book:before {
  content: "\f02d";
}
.fa-bookmark:before {
  content: "\f02e";
}
.fa-print:before {
  content: "\f02f";
}
.fa-camera:before {
  content: "\f030";
}
.fa-font:before {
  content: "\f031";
}
.fa-bold:before {
  content: "\f032";
}
.fa-italic:before {
  content: "\f033";
}
.fa-text-height:before {
  content: "\f034";
}
.fa-text-width:before {
  content: "\f035";
}
.fa-align-left:before {
  content: "\f036";
}
.fa-align-center:before {
  content: "\f037";
}
.fa-align-right:before {
  content: "\f038";
}
.fa-align-justify:before {
  content: "\f039";
}
.fa-list:before {
  content: "\f03a";
}
.fa-dedent:before,
.fa-outdent:before {
  content: "\f03b";
}
.fa-indent:before {
  content: "\f03c";
}
.fa-video-camera:before {
  content: "\f03d";
}
.fa-photo:before,
.fa-image:before,
.fa-picture-o:before {
  content: "\f03e";
}
.fa-pencil:before {
  content: "\f040";
}
.fa-map-marker:before {
  content: "\f041";
}
.fa-adjust:before {
  content: "\f042";
}
.fa-tint:before {
  content: "\f043";
}
.fa-edit:before,
.fa-pencil-square-o:before {
  content: "\f044";
}
.fa-share-square-o:before {
  content: "\f045";
}
.fa-check-square-o:before {
  content: "\f046";
}
.fa-arrows:before {
  content: "\f047";
}
.fa-step-backward:before {
  content: "\f048";
}
.fa-fast-backward:before {
  content: "\f049";
}
.fa-backward:before {
  content: "\f04a";
}
.fa-play:before {
  content: "\f04b";
}
.fa-pause:before {
  content: "\f04c";
}
.fa-stop:before {
  content: "\f04d";
}
.fa-forward:before {
  content: "\f04e";
}
.fa-fast-forward:before {
  content: "\f050";
}
.fa-step-forward:before {
  content: "\f051";
}
.fa-eject:before {
  content: "\f052";
}
.fa-chevron-left:before {
  content: "\f053";
}
.fa-chevron-right:before {
  content: "\f054";
}
.fa-plus-circle:before {
  content: "\f055";
}
.fa-minus-circle:before {
  content: "\f056";
}
.fa-times-circle:before {
  content: "\f057";
}
.fa-check-circle:before {
  content: "\f058";
}
.fa-question-circle:before {
  content: "\f059";
}
.fa-info-circle:before {
  content: "\f05a";
}
.fa-crosshairs:before {
  content: "\f05b";
}
.fa-times-circle-o:before {
  content: "\f05c";
}
.fa-check-circle-o:before {
  content: "\f05d";
}
.fa-ban:before {
  content: "\f05e";
}
.fa-arrow-left:before {
  content: "\f060";
}
.fa-arrow-right:before {
  content: "\f061";
}
.fa-arrow-up:before {
  content: "\f062";
}
.fa-arrow-down:before {
  content: "\f063";
}
.fa-mail-forward:before,
.fa-share:before {
  content: "\f064";
}
.fa-expand:before {
  content: "\f065";
}
.fa-compress:before {
  content: "\f066";
}
.fa-plus:before {
  content: "\f067";
}
.fa-minus:before {
  content: "\f068";
}
.fa-asterisk:before {
  content: "\f069";
}
.fa-exclamation-circle:before {
  content: "\f06a";
}
.fa-gift:before {
  content: "\f06b";
}
.fa-leaf:before {
  content: "\f06c";
}
.fa-fire:before {
  content: "\f06d";
}
.fa-eye:before {
  content: "\f06e";
}
.fa-eye-slash:before {
  content: "\f070";
}
.fa-warning:before,
.fa-exclamation-triangle:before {
  content: "\f071";
}
.fa-plane:before {
  content: "\f072";
}
.fa-calendar:before {
  content: "\f073";
}
.fa-random:before {
  content: "\f074";
}
.fa-comment:before {
  content: "\f075";
}
.fa-magnet:before {
  content: "\f076";
}
.fa-chevron-up:before {
  content: "\f077";
}
.fa-chevron-down:before {
  content: "\f078";
}
.fa-retweet:before {
  content: "\f079";
}
.fa-shopping-cart:before {
  content: "\f07a";
}
.fa-folder:before {
  content: "\f07b";
}
.fa-folder-open:before {
  content: "\f07c";
}
.fa-arrows-v:before {
  content: "\f07d";
}
.fa-arrows-h:before {
  content: "\f07e";
}
.fa-bar-chart-o:before,
.fa-bar-chart:before {
  content: "\f080";
}
.fa-twitter-square:before {
  content: "\f081";
}
.fa-facebook-square:before {
  content: "\f082";
}
.fa-camera-retro:before {
  content: "\f083";
}
.fa-key:before {
  content: "\f084";
}
.fa-gears:before,
.fa-cogs:before {
  content: "\f085";
}
.fa-comments:before {
  content: "\f086";
}
.fa-thumbs-o-up:before {
  content: "\f087";
}
.fa-thumbs-o-down:before {
  content: "\f088";
}
.fa-star-half:before {
  content: "\f089";
}
.fa-heart-o:before {
  content: "\f08a";
}
.fa-sign-out:before {
  content: "\f08b";
}
.fa-linkedin-square:before {
  content: "\f08c";
}
.fa-thumb-tack:before {
  content: "\f08d";
}
.fa-external-link:before {
  content: "\f08e";
}
.fa-sign-in:before {
  content: "\f090";
}
.fa-trophy:before {
  content: "\f091";
}
.fa-github-square:before {
  content: "\f092";
}
.fa-upload:before {
  content: "\f093";
}
.fa-lemon-o:before {
  content: "\f094";
}
.fa-phone:before {
  content: "\f095";
}
.fa-square-o:before {
  content: "\f096";
}
.fa-bookmark-o:before {
  content: "\f097";
}
.fa-phone-square:before {
  content: "\f098";
}
.fa-twitter:before {
  content: "\f099";
}
.fa-facebook-f:before,
.fa-facebook:before {
  content: "\f09a";
}
.fa-github:before {
  content: "\f09b";
}
.fa-unlock:before {
  content: "\f09c";
}
.fa-credit-card:before {
  content: "\f09d";
}
.fa-feed:before,
.fa-rss:before {
  content: "\f09e";
}
.fa-hdd-o:before {
  content: "\f0a0";
}
.fa-bullhorn:before {
  content: "\f0a1";
}
.fa-bell:before {
  content: "\f0f3";
}
.fa-certificate:before {
  content: "\f0a3";
}
.fa-hand-o-right:before {
  content: "\f0a4";
}
.fa-hand-o-left:before {
  content: "\f0a5";
}
.fa-hand-o-up:before {
  content: "\f0a6";
}
.fa-hand-o-down:before {
  content: "\f0a7";
}
.fa-arrow-circle-left:before {
  content: "\f0a8";
}
.fa-arrow-circle-right:before {
  content: "\f0a9";
}
.fa-arrow-circle-up:before {
  content: "\f0aa";
}
.fa-arrow-circle-down:before {
  content: "\f0ab";
}
.fa-globe:before {
  content: "\f0ac";
}
.fa-wrench:before {
  content: "\f0ad";
}
.fa-tasks:before {
  content: "\f0ae";
}
.fa-filter:before {
  content: "\f0b0";
}
.fa-briefcase:before {
  content: "\f0b1";
}
.fa-arrows-alt:before {
  content: "\f0b2";
}
.fa-group:before,
.fa-users:before {
  content: "\f0c0";
}
.fa-chain:before,
.fa-link:before {
  content: "\f0c1";
}
.fa-cloud:before {
  content: "\f0c2";
}
.fa-flask:before {
  content: "\f0c3";
}
.fa-cut:before,
.fa-scissors:before {
  content: "\f0c4";
}
.fa-copy:before,
.fa-files-o:before {
  content: "\f0c5";
}
.fa-paperclip:before {
  content: "\f0c6";
}
.fa-save:before,
.fa-floppy-o:before {
  content: "\f0c7";
}
.fa-square:before {
  content: "\f0c8";
}
.fa-navicon:before,
.fa-reorder:before,
.fa-bars:before {
  content: "\f0c9";
}
.fa-list-ul:before {
  content: "\f0ca";
}
.fa-list-ol:before {
  content: "\f0cb";
}
.fa-strikethrough:before {
  content: "\f0cc";
}
.fa-underline:before {
  content: "\f0cd";
}
.fa-table:before {
  content: "\f0ce";
}
.fa-magic:before {
  content: "\f0d0";
}
.fa-truck:before {
  content: "\f0d1";
}
.fa-pinterest:before {
  content: "\f0d2";
}
.fa-pinterest-square:before {
  content: "\f0d3";
}
.fa-google-plus-square:before {
  content: "\f0d4";
}
.fa-google-plus:before {
  content: "\f0d5";
}
.fa-money:before {
  content: "\f0d6";
}
.fa-caret-down:before {
  content: "\f0d7";
}
.fa-caret-up:before {
  content: "\f0d8";
}
.fa-caret-left:before {
  content: "\f0d9";
}
.fa-caret-right:before {
  content: "\f0da";
}
.fa-columns:before {
  content: "\f0db";
}
.fa-unsorted:before,
.fa-sort:before {
  content: "\f0dc";
}
.fa-sort-down:before,
.fa-sort-desc:before {
  content: "\f0dd";
}
.fa-sort-up:before,
.fa-sort-asc:before {
  content: "\f0de";
}
.fa-envelope:before {
  content: "\f0e0";
}
.fa-linkedin:before {
  content: "\f0e1";
}
.fa-rotate-left:before,
.fa-undo:before {
  content: "\f0e2";
}
.fa-legal:before,
.fa-gavel:before {
  content: "\f0e3";
}
.fa-dashboard:before,
.fa-tachometer:before {
  content: "\f0e4";
}
.fa-comment-o:before {
  content: "\f0e5";
}
.fa-comments-o:before {
  content: "\f0e6";
}
.fa-flash:before,
.fa-bolt:before {
  content: "\f0e7";
}
.fa-sitemap:before {
  content: "\f0e8";
}
.fa-umbrella:before {
  content: "\f0e9";
}
.fa-paste:before,
.fa-clipboard:before {
  content: "\f0ea";
}
.fa-lightbulb-o:before {
  content: "\f0eb";
}
.fa-exchange:before {
  content: "\f0ec";
}
.fa-cloud-download:before {
  content: "\f0ed";
}
.fa-cloud-upload:before {
  content: "\f0ee";
}
.fa-user-md:before {
  content: "\f0f0";
}
.fa-stethoscope:before {
  content: "\f0f1";
}
.fa-suitcase:before {
  content: "\f0f2";
}
.fa-bell-o:before {
  content: "\f0a2";
}
.fa-coffee:before {
  content: "\f0f4";
}
.fa-cutlery:before {
  content: "\f0f5";
}
.fa-file-text-o:before {
  content: "\f0f6";
}
.fa-building-o:before {
  content: "\f0f7";
}
.fa-hospital-o:before {
  content: "\f0f8";
}
.fa-ambulance:before {
  content: "\f0f9";
}
.fa-medkit:before {
  content: "\f0fa";
}
.fa-fighter-jet:before {
  content: "\f0fb";
}
.fa-beer:before {
  content: "\f0fc";
}
.fa-h-square:before {
  content: "\f0fd";
}
.fa-plus-square:before {
  content: "\f0fe";
}
.fa-angle-double-left:before {
  content: "\f100";
}
.fa-angle-double-right:before {
  content: "\f101";
}
.fa-angle-double-up:before {
  content: "\f102";
}
.fa-angle-double-down:before {
  content: "\f103";
}
.fa-angle-left:before {
  content: "\f104";
}
.fa-angle-right:before {
  content: "\f105";
}
.fa-angle-up:before {
  content: "\f106";
}
.fa-angle-down:before {
  content: "\f107";
}
.fa-desktop:before {
  content: "\f108";
}
.fa-laptop:before {
  content: "\f109";
}
.fa-tablet:before {
  content: "\f10a";
}
.fa-mobile-phone:before,
.fa-mobile:before {
  content: "\f10b";
}
.fa-circle-o:before {
  content: "\f10c";
}
.fa-quote-left:before {
  content: "\f10d";
}
.fa-quote-right:before {
  content: "\f10e";
}
.fa-spinner:before {
  content: "\f110";
}
.fa-circle:before {
  content: "\f111";
}
.fa-mail-reply:before,
.fa-reply:before {
  content: "\f112";
}
.fa-github-alt:before {
  content: "\f113";
}
.fa-folder-o:before {
  content: "\f114";
}
.fa-folder-open-o:before {
  content: "\f115";
}
.fa-smile-o:before {
  content: "\f118";
}
.fa-frown-o:before {
  content: "\f119";
}
.fa-meh-o:before {
  content: "\f11a";
}
.fa-gamepad:before {
  content: "\f11b";
}
.fa-keyboard-o:before {
  content: "\f11c";
}
.fa-flag-o:before {
  content: "\f11d";
}
.fa-flag-checkered:before {
  content: "\f11e";
}
.fa-terminal:before {
  content: "\f120";
}
.fa-code:before {
  content: "\f121";
}
.fa-mail-reply-all:before,
.fa-reply-all:before {
  content: "\f122";
}
.fa-star-half-empty:before,
.fa-star-half-full:before,
.fa-star-half-o:before {
  content: "\f123";
}
.fa-location-arrow:before {
  content: "\f124";
}
.fa-crop:before {
  content: "\f125";
}
.fa-code-fork:before {
  content: "\f126";
}
.fa-unlink:before,
.fa-chain-broken:before {
  content: "\f127";
}
.fa-question:before {
  content: "\f128";
}
.fa-info:before {
  content: "\f129";
}
.fa-exclamation:before {
  content: "\f12a";
}
.fa-superscript:before {
  content: "\f12b";
}
.fa-subscript:before {
  content: "\f12c";
}
.fa-eraser:before {
  content: "\f12d";
}
.fa-puzzle-piece:before {
  content: "\f12e";
}
.fa-microphone:before {
  content: "\f130";
}
.fa-microphone-slash:before {
  content: "\f131";
}
.fa-shield:before {
  content: "\f132";
}
.fa-calendar-o:before {
  content: "\f133";
}
.fa-fire-extinguisher:before {
  content: "\f134";
}
.fa-rocket:before {
  content: "\f135";
}
.fa-maxcdn:before {
  content: "\f136";
}
.fa-chevron-circle-left:before {
  content: "\f137";
}
.fa-chevron-circle-right:before {
  content: "\f138";
}
.fa-chevron-circle-up:before {
  content: "\f139";
}
.fa-chevron-circle-down:before {
  content: "\f13a";
}
.fa-html5:before {
  content: "\f13b";
}
.fa-css3:before {
  content: "\f13c";
}
.fa-anchor:before {
  content: "\f13d";
}
.fa-unlock-alt:before {
  content: "\f13e";
}
.fa-bullseye:before {
  content: "\f140";
}
.fa-ellipsis-h:before {
  content: "\f141";
}
.fa-ellipsis-v:before {
  content: "\f142";
}
.fa-rss-square:before {
  content: "\f143";
}
.fa-play-circle:before {
  content: "\f144";
}
.fa-ticket:before {
  content: "\f145";
}
.fa-minus-square:before {
  content: "\f146";
}
.fa-minus-square-o:before {
  content: "\f147";
}
.fa-level-up:before {
  content: "\f148";
}
.fa-level-down:before {
  content: "\f149";
}
.fa-check-square:before {
  content: "\f14a";
}
.fa-pencil-square:before {
  content: "\f14b";
}
.fa-external-link-square:before {
  content: "\f14c";
}
.fa-share-square:before {
  content: "\f14d";
}
.fa-compass:before {
  content: "\f14e";
}
.fa-toggle-down:before,
.fa-caret-square-o-down:before {
  content: "\f150";
}
.fa-toggle-up:before,
.fa-caret-square-o-up:before {
  content: "\f151";
}
.fa-toggle-right:before,
.fa-caret-square-o-right:before {
  content: "\f152";
}
.fa-euro:before,
.fa-eur:before {
  content: "\f153";
}
.fa-gbp:before {
  content: "\f154";
}
.fa-dollar:before,
.fa-usd:before {
  content: "\f155";
}
.fa-rupee:before,
.fa-inr:before {
  content: "\f156";
}
.fa-cny:before,
.fa-rmb:before,
.fa-yen:before,
.fa-jpy:before {
  content: "\f157";
}
.fa-ruble:before,
.fa-rouble:before,
.fa-rub:before {
  content: "\f158";
}
.fa-won:before,
.fa-krw:before {
  content: "\f159";
}
.fa-bitcoin:before,
.fa-btc:before {
  content: "\f15a";
}
.fa-file:before {
  content: "\f15b";
}
.fa-file-text:before {
  content: "\f15c";
}
.fa-sort-alpha-asc:before {
  content: "\f15d";
}
.fa-sort-alpha-desc:before {
  content: "\f15e";
}
.fa-sort-amount-asc:before {
  content: "\f160";
}
.fa-sort-amount-desc:before {
  content: "\f161";
}
.fa-sort-numeric-asc:before {
  content: "\f162";
}
.fa-sort-numeric-desc:before {
  content: "\f163";
}
.fa-thumbs-up:before {
  content: "\f164";
}
.fa-thumbs-down:before {
  content: "\f165";
}
.fa-youtube-square:before {
  content: "\f166";
}
.fa-youtube:before {
  content: "\f167";
}
.fa-xing:before {
  content: "\f168";
}
.fa-xing-square:before {
  content: "\f169";
}
.fa-youtube-play:before {
  content: "\f16a";
}
.fa-dropbox:before {
  content: "\f16b";
}
.fa-stack-overflow:before {
  content: "\f16c";
}
.fa-instagram:before {
  content: "\f16d";
}
.fa-flickr:before {
  content: "\f16e";
}
.fa-adn:before {
  content: "\f170";
}
.fa-bitbucket:before {
  content: "\f171";
}
.fa-bitbucket-square:before {
  content: "\f172";
}
.fa-tumblr:before {
  content: "\f173";
}
.fa-tumblr-square:before {
  content: "\f174";
}
.fa-long-arrow-down:before {
  content: "\f175";
}
.fa-long-arrow-up:before {
  content: "\f176";
}
.fa-long-arrow-left:before {
  content: "\f177";
}
.fa-long-arrow-right:before {
  content: "\f178";
}
.fa-apple:before {
  content: "\f179";
}
.fa-windows:before {
  content: "\f17a";
}
.fa-android:before {
  content: "\f17b";
}
.fa-linux:before {
  content: "\f17c";
}
.fa-dribbble:before {
  content: "\f17d";
}
.fa-skype:before {
  content: "\f17e";
}
.fa-foursquare:before {
  content: "\f180";
}
.fa-trello:before {
  content: "\f181";
}
.fa-female:before {
  content: "\f182";
}
.fa-male:before {
  content: "\f183";
}
.fa-gittip:before,
.fa-gratipay:before {
  content: "\f184";
}
.fa-sun-o:before {
  content: "\f185";
}
.fa-moon-o:before {
  content: "\f186";
}
.fa-archive:before {
  content: "\f187";
}
.fa-bug:before {
  content: "\f188";
}
.fa-vk:before {
  content: "\f189";
}
.fa-weibo:before {
  content: "\f18a";
}
.fa-renren:before {
  content: "\f18b";
}
.fa-pagelines:before {
  content: "\f18c";
}
.fa-stack-exchange:before {
  content: "\f18d";
}
.fa-arrow-circle-o-right:before {
  content: "\f18e";
}
.fa-arrow-circle-o-left:before {
  content: "\f190";
}
.fa-toggle-left:before,
.fa-caret-square-o-left:before {
  content: "\f191";
}
.fa-dot-circle-o:before {
  content: "\f192";
}
.fa-wheelchair:before {
  content: "\f193";
}
.fa-vimeo-square:before {
  content: "\f194";
}
.fa-turkish-lira:before,
.fa-try:before {
  content: "\f195";
}
.fa-plus-square-o:before {
  content: "\f196";
}
.fa-space-shuttle:before {
  content: "\f197";
}
.fa-slack:before {
  content: "\f198";
}
.fa-envelope-square:before {
  content: "\f199";
}
.fa-wordpress:before {
  content: "\f19a";
}
.fa-openid:before {
  content: "\f19b";
}
.fa-institution:before,
.fa-bank:before,
.fa-university:before {
  content: "\f19c";
}
.fa-mortar-board:before,
.fa-graduation-cap:before {
  content: "\f19d";
}
.fa-yahoo:before {
  content: "\f19e";
}
.fa-google:before {
  content: "\f1a0";
}
.fa-reddit:before {
  content: "\f1a1";
}
.fa-reddit-square:before {
  content: "\f1a2";
}
.fa-stumbleupon-circle:before {
  content: "\f1a3";
}
.fa-stumbleupon:before {
  content: "\f1a4";
}
.fa-delicious:before {
  content: "\f1a5";
}
.fa-digg:before {
  content: "\f1a6";
}
.fa-pied-piper-pp:before {
  content: "\f1a7";
}
.fa-pied-piper-alt:before {
  content: "\f1a8";
}
.fa-drupal:before {
  content: "\f1a9";
}
.fa-joomla:before {
  content: "\f1aa";
}
.fa-language:before {
  content: "\f1ab";
}
.fa-fax:before {
  content: "\f1ac";
}
.fa-building:before {
  content: "\f1ad";
}
.fa-child:before {
  content: "\f1ae";
}
.fa-paw:before {
  content: "\f1b0";
}
.fa-spoon:before {
  content: "\f1b1";
}
.fa-cube:before {
  content: "\f1b2";
}
.fa-cubes:before {
  content: "\f1b3";
}
.fa-behance:before {
  content: "\f1b4";
}
.fa-behance-square:before {
  content: "\f1b5";
}
.fa-steam:before {
  content: "\f1b6";
}
.fa-steam-square:before {
  content: "\f1b7";
}
.fa-recycle:before {
  content: "\f1b8";
}
.fa-automobile:before,
.fa-car:before {
  content: "\f1b9";
}
.fa-cab:before,
.fa-taxi:before {
  content: "\f1ba";
}
.fa-tree:before {
  content: "\f1bb";
}
.fa-spotify:before {
  content: "\f1bc";
}
.fa-deviantart:before {
  content: "\f1bd";
}
.fa-soundcloud:before {
  content: "\f1be";
}
.fa-database:before {
  content: "\f1c0";
}
.fa-file-pdf-o:before {
  content: "\f1c1";
}
.fa-file-word-o:before {
  content: "\f1c2";
}
.fa-file-excel-o:before {
  content: "\f1c3";
}
.fa-file-powerpoint-o:before {
  content: "\f1c4";
}
.fa-file-photo-o:before,
.fa-file-picture-o:before,
.fa-file-image-o:before {
  content: "\f1c5";
}
.fa-file-zip-o:before,
.fa-file-archive-o:before {
  content: "\f1c6";
}
.fa-file-sound-o:before,
.fa-file-audio-o:before {
  content: "\f1c7";
}
.fa-file-movie-o:before,
.fa-file-video-o:before {
  content: "\f1c8";
}
.fa-file-code-o:before {
  content: "\f1c9";
}
.fa-vine:before {
  content: "\f1ca";
}
.fa-codepen:before {
  content: "\f1cb";
}
.fa-jsfiddle:before {
  content: "\f1cc";
}
.fa-life-bouy:before,
.fa-life-buoy:before,
.fa-life-saver:before,
.fa-support:before,
.fa-life-ring:before {
  content: "\f1cd";
}
.fa-circle-o-notch:before {
  content: "\f1ce";
}
.fa-ra:before,
.fa-resistance:before,
.fa-rebel:before {
  content: "\f1d0";
}
.fa-ge:before,
.fa-empire:before {
  content: "\f1d1";
}
.fa-git-square:before {
  content: "\f1d2";
}
.fa-git:before {
  content: "\f1d3";
}
.fa-y-combinator-square:before,
.fa-yc-square:before,
.fa-hacker-news:before {
  content: "\f1d4";
}
.fa-tencent-weibo:before {
  content: "\f1d5";
}
.fa-qq:before {
  content: "\f1d6";
}
.fa-wechat:before,
.fa-weixin:before {
  content: "\f1d7";
}
.fa-send:before,
.fa-paper-plane:before {
  content: "\f1d8";
}
.fa-send-o:before,
.fa-paper-plane-o:before {
  content: "\f1d9";
}
.fa-history:before {
  content: "\f1da";
}
.fa-circle-thin:before {
  content: "\f1db";
}
.fa-header:before {
  content: "\f1dc";
}
.fa-paragraph:before {
  content: "\f1dd";
}
.fa-sliders:before {
  content: "\f1de";
}
.fa-share-alt:before {
  content: "\f1e0";
}
.fa-share-alt-square:before {
  content: "\f1e1";
}
.fa-bomb:before {
  content: "\f1e2";
}
.fa-soccer-ball-o:before,
.fa-futbol-o:before {
  content: "\f1e3";
}
.fa-tty:before {
  content: "\f1e4";
}
.fa-binoculars:before {
  content: "\f1e5";
}
.fa-plug:before {
  content: "\f1e6";
}
.fa-slideshare:before {
  content: "\f1e7";
}
.fa-twitch:before {
  content: "\f1e8";
}
.fa-yelp:before {
  content: "\f1e9";
}
.fa-newspaper-o:before {
  content: "\f1ea";
}
.fa-wifi:before {
  content: "\f1eb";
}
.fa-calculator:before {
  content: "\f1ec";
}
.fa-paypal:before {
  content: "\f1ed";
}
.fa-google-wallet:before {
  content: "\f1ee";
}
.fa-cc-visa:before {
  content: "\f1f0";
}
.fa-cc-mastercard:before {
  content: "\f1f1";
}
.fa-cc-discover:before {
  content: "\f1f2";
}
.fa-cc-amex:before {
  content: "\f1f3";
}
.fa-cc-paypal:before {
  content: "\f1f4";
}
.fa-cc-stripe:before {
  content: "\f1f5";
}
.fa-bell-slash:before {
  content: "\f1f6";
}
.fa-bell-slash-o:before {
  content: "\f1f7";
}
.fa-trash:before {
  content: "\f1f8";
}
.fa-copyright:before {
  content: "\f1f9";
}
.fa-at:before {
  content: "\f1fa";
}
.fa-eyedropper:before {
  content: "\f1fb";
}
.fa-paint-brush:before {
  content: "\f1fc";
}
.fa-birthday-cake:before {
  content: "\f1fd";
}
.fa-area-chart:before {
  content: "\f1fe";
}
.fa-pie-chart:before {
  content: "\f200";
}
.fa-line-chart:before {
  content: "\f201";
}
.fa-lastfm:before {
  content: "\f202";
}
.fa-lastfm-square:before {
  content: "\f203";
}
.fa-toggle-off:before {
  content: "\f204";
}
.fa-toggle-on:before {
  content: "\f205";
}
.fa-bicycle:before {
  content: "\f206";
}
.fa-bus:before {
  content: "\f207";
}
.fa-ioxhost:before {
  content: "\f208";
}
.fa-angellist:before {
  content: "\f209";
}
.fa-cc:before {
  content: "\f20a";
}
.fa-shekel:before,
.fa-sheqel:before,
.fa-ils:before {
  content: "\f20b";
}
.fa-meanpath:before {
  content: "\f20c";
}
.fa-buysellads:before {
  content: "\f20d";
}
.fa-connectdevelop:before {
  content: "\f20e";
}
.fa-dashcube:before {
  content: "\f210";
}
.fa-forumbee:before {
  content: "\f211";
}
.fa-leanpub:before {
  content: "\f212";
}
.fa-sellsy:before {
  content: "\f213";
}
.fa-shirtsinbulk:before {
  content: "\f214";
}
.fa-simplybuilt:before {
  content: "\f215";
}
.fa-skyatlas:before {
  content: "\f216";
}
.fa-cart-plus:before {
  content: "\f217";
}
.fa-cart-arrow-down:before {
  content: "\f218";
}
.fa-diamond:before {
  content: "\f219";
}
.fa-ship:before {
  content: "\f21a";
}
.fa-user-secret:before {
  content: "\f21b";
}
.fa-motorcycle:before {
  content: "\f21c";
}
.fa-street-view:before {
  content: "\f21d";
}
.fa-heartbeat:before {
  content: "\f21e";
}
.fa-venus:before {
  content: "\f221";
}
.fa-mars:before {
  content: "\f222";
}
.fa-mercury:before {
  content: "\f223";
}
.fa-intersex:before,
.fa-transgender:before {
  content: "\f224";
}
.fa-transgender-alt:before {
  content: "\f225";
}
.fa-venus-double:before {
  content: "\f226";
}
.fa-mars-double:before {
  content: "\f227";
}
.fa-venus-mars:before {
  content: "\f228";
}
.fa-mars-stroke:before {
  content: "\f229";
}
.fa-mars-stroke-v:before {
  content: "\f22a";
}
.fa-mars-stroke-h:before {
  content: "\f22b";
}
.fa-neuter:before {
  content: "\f22c";
}
.fa-genderless:before {
  content: "\f22d";
}
.fa-facebook-official:before {
  content: "\f230";
}
.fa-pinterest-p:before {
  content: "\f231";
}
.fa-whatsapp:before {
  content: "\f232";
}
.fa-server:before {
  content: "\f233";
}
.fa-user-plus:before {
  content: "\f234";
}
.fa-user-times:before {
  content: "\f235";
}
.fa-hotel:before,
.fa-bed:before {
  content: "\f236";
}
.fa-viacoin:before {
  content: "\f237";
}
.fa-train:before {
  content: "\f238";
}
.fa-subway:before {
  content: "\f239";
}
.fa-medium:before {
  content: "\f23a";
}
.fa-yc:before,
.fa-y-combinator:before {
  content: "\f23b";
}
.fa-optin-monster:before {
  content: "\f23c";
}
.fa-opencart:before {
  content: "\f23d";
}
.fa-expeditedssl:before {
  content: "\f23e";
}
.fa-battery-4:before,
.fa-battery:before,
.fa-battery-full:before {
  content: "\f240";
}
.fa-battery-3:before,
.fa-battery-three-quarters:before {
  content: "\f241";
}
.fa-battery-2:before,
.fa-battery-half:before {
  content: "\f242";
}
.fa-battery-1:before,
.fa-battery-quarter:before {
  content: "\f243";
}
.fa-battery-0:before,
.fa-battery-empty:before {
  content: "\f244";
}
.fa-mouse-pointer:before {
  content: "\f245";
}
.fa-i-cursor:before {
  content: "\f246";
}
.fa-object-group:before {
  content: "\f247";
}
.fa-object-ungroup:before {
  content: "\f248";
}
.fa-sticky-note:before {
  content: "\f249";
}
.fa-sticky-note-o:before {
  content: "\f24a";
}
.fa-cc-jcb:before {
  content: "\f24b";
}
.fa-cc-diners-club:before {
  content: "\f24c";
}
.fa-clone:before {
  content: "\f24d";
}
.fa-balance-scale:before {
  content: "\f24e";
}
.fa-hourglass-o:before {
  content: "\f250";
}
.fa-hourglass-1:before,
.fa-hourglass-start:before {
  content: "\f251";
}
.fa-hourglass-2:before,
.fa-hourglass-half:before {
  content: "\f252";
}
.fa-hourglass-3:before,
.fa-hourglass-end:before {
  content: "\f253";
}
.fa-hourglass:before {
  content: "\f254";
}
.fa-hand-grab-o:before,
.fa-hand-rock-o:before {
  content: "\f255";
}
.fa-hand-stop-o:before,
.fa-hand-paper-o:before {
  content: "\f256";
}
.fa-hand-scissors-o:before {
  content: "\f257";
}
.fa-hand-lizard-o:before {
  content: "\f258";
}
.fa-hand-spock-o:before {
  content: "\f259";
}
.fa-hand-pointer-o:before {
  content: "\f25a";
}
.fa-hand-peace-o:before {
  content: "\f25b";
}
.fa-trademark:before {
  content: "\f25c";
}
.fa-registered:before {
  content: "\f25d";
}
.fa-creative-commons:before {
  content: "\f25e";
}
.fa-gg:before {
  content: "\f260";
}
.fa-gg-circle:before {
  content: "\f261";
}
.fa-tripadvisor:before {
  content: "\f262";
}
.fa-odnoklassniki:before {
  content: "\f263";
}
.fa-odnoklassniki-square:before {
  content: "\f264";
}
.fa-get-pocket:before {
  content: "\f265";
}
.fa-wikipedia-w:before {
  content: "\f266";
}
.fa-safari:before {
  content: "\f267";
}
.fa-chrome:before {
  content: "\f268";
}
.fa-firefox:before {
  content: "\f269";
}
.fa-opera:before {
  content: "\f26a";
}
.fa-internet-explorer:before {
  content: "\f26b";
}
.fa-tv:before,
.fa-television:before {
  content: "\f26c";
}
.fa-contao:before {
  content: "\f26d";
}
.fa-500px:before {
  content: "\f26e";
}
.fa-amazon:before {
  content: "\f270";
}
.fa-calendar-plus-o:before {
  content: "\f271";
}
.fa-calendar-minus-o:before {
  content: "\f272";
}
.fa-calendar-times-o:before {
  content: "\f273";
}
.fa-calendar-check-o:before {
  content: "\f274";
}
.fa-industry:before {
  content: "\f275";
}
.fa-map-pin:before {
  content: "\f276";
}
.fa-map-signs:before {
  content: "\f277";
}
.fa-map-o:before {
  content: "\f278";
}
.fa-map:before {
  content: "\f279";
}
.fa-commenting:before {
  content: "\f27a";
}
.fa-commenting-o:before {
  content: "\f27b";
}
.fa-houzz:before {
  content: "\f27c";
}
.fa-vimeo:before {
  content: "\f27d";
}
.fa-black-tie:before {
  content: "\f27e";
}
.fa-fonticons:before {
  content: "\f280";
}
.fa-reddit-alien:before {
  content: "\f281";
}
.fa-edge:before {
  content: "\f282";
}
.fa-credit-card-alt:before {
  content: "\f283";
}
.fa-codiepie:before {
  content: "\f284";
}
.fa-modx:before {
  content: "\f285";
}
.fa-fort-awesome:before {
  content: "\f286";
}
.fa-usb:before {
  content: "\f287";
}
.fa-product-hunt:before {
  content: "\f288";
}
.fa-mixcloud:before {
  content: "\f289";
}
.fa-scribd:before {
  content: "\f28a";
}
.fa-pause-circle:before {
  content: "\f28b";
}
.fa-pause-circle-o:before {
  content: "\f28c";
}
.fa-stop-circle:before {
  content: "\f28d";
}
.fa-stop-circle-o:before {
  content: "\f28e";
}
.fa-shopping-bag:before {
  content: "\f290";
}
.fa-shopping-basket:before {
  content: "\f291";
}
.fa-hashtag:before {
  content: "\f292";
}
.fa-bluetooth:before {
  content: "\f293";
}
.fa-bluetooth-b:before {
  content: "\f294";
}
.fa-percent:before {
  content: "\f295";
}
.fa-gitlab:before {
  content: "\f296";
}
.fa-wpbeginner:before {
  content: "\f297";
}
.fa-wpforms:before {
  content: "\f298";
}
.fa-envira:before {
  content: "\f299";
}
.fa-universal-access:before {
  content: "\f29a";
}
.fa-wheelchair-alt:before {
  content: "\f29b";
}
.fa-question-circle-o:before {
  content: "\f29c";
}
.fa-blind:before {
  content: "\f29d";
}
.fa-audio-description:before {
  content: "\f29e";
}
.fa-volume-control-phone:before {
  content: "\f2a0";
}
.fa-braille:before {
  content: "\f2a1";
}
.fa-assistive-listening-systems:before {
  content: "\f2a2";
}
.fa-asl-interpreting:before,
.fa-american-sign-language-interpreting:before {
  content: "\f2a3";
}
.fa-deafness:before,
.fa-hard-of-hearing:before,
.fa-deaf:before {
  content: "\f2a4";
}
.fa-glide:before {
  content: "\f2a5";
}
.fa-glide-g:before {
  content: "\f2a6";
}
.fa-signing:before,
.fa-sign-language:before {
  content: "\f2a7";
}
.fa-low-vision:before {
  content: "\f2a8";
}
.fa-viadeo:before {
  content: "\f2a9";
}
.fa-viadeo-square:before {
  content: "\f2aa";
}
.fa-snapchat:before {
  content: "\f2ab";
}
.fa-snapchat-ghost:before {
  content: "\f2ac";
}
.fa-snapchat-square:before {
  content: "\f2ad";
}
.fa-pied-piper:before {
  content: "\f2ae";
}
.fa-first-order:before {
  content: "\f2b0";
}
.fa-yoast:before {
  content: "\f2b1";
}
.fa-themeisle:before {
  content: "\f2b2";
}
.fa-google-plus-circle:before,
.fa-google-plus-official:before {
  content: "\f2b3";
}
.fa-fa:before,
.fa-font-awesome:before {
  content: "\f2b4";
}
.fa-handshake-o:before {
  content: "\f2b5";
}
.fa-envelope-open:before {
  content: "\f2b6";
}
.fa-envelope-open-o:before {
  content: "\f2b7";
}
.fa-linode:before {
  content: "\f2b8";
}
.fa-address-book:before {
  content: "\f2b9";
}
.fa-address-book-o:before {
  content: "\f2ba";
}
.fa-vcard:before,
.fa-address-card:before {
  content: "\f2bb";
}
.fa-vcard-o:before,
.fa-address-card-o:before {
  content: "\f2bc";
}
.fa-user-circle:before {
  content: "\f2bd";
}
.fa-user-circle-o:before {
  content: "\f2be";
}
.fa-user-o:before {
  content: "\f2c0";
}
.fa-id-badge:before {
  content: "\f2c1";
}
.fa-drivers-license:before,
.fa-id-card:before {
  content: "\f2c2";
}
.fa-drivers-license-o:before,
.fa-id-card-o:before {
  content: "\f2c3";
}
.fa-quora:before {
  content: "\f2c4";
}
.fa-free-code-camp:before {
  content: "\f2c5";
}
.fa-telegram:before {
  content: "\f2c6";
}
.fa-thermometer-4:before,
.fa-thermometer:before,
.fa-thermometer-full:before {
  content: "\f2c7";
}
.fa-thermometer-3:before,
.fa-thermometer-three-quarters:before {
  content: "\f2c8";
}
.fa-thermometer-2:before,
.fa-thermometer-half:before {
  content: "\f2c9";
}
.fa-thermometer-1:before,
.fa-thermometer-quarter:before {
  content: "\f2ca";
}
.fa-thermometer-0:before,
.fa-thermometer-empty:before {
  content: "\f2cb";
}
.fa-shower:before {
  content: "\f2cc";
}
.fa-bathtub:before,
.fa-s15:before,
.fa-bath:before {
  content: "\f2cd";
}
.fa-podcast:before {
  content: "\f2ce";
}
.fa-window-maximize:before {
  content: "\f2d0";
}
.fa-window-minimize:before {
  content: "\f2d1";
}
.fa-window-restore:before {
  content: "\f2d2";
}
.fa-times-rectangle:before,
.fa-window-close:before {
  content: "\f2d3";
}
.fa-times-rectangle-o:before,
.fa-window-close-o:before {
  content: "\f2d4";
}
.fa-bandcamp:before {
  content: "\f2d5";
}
.fa-grav:before {
  content: "\f2d6";
}
.fa-etsy:before {
  content: "\f2d7";
}
.fa-imdb:before {
  content: "\f2d8";
}
.fa-ravelry:before {
  content: "\f2d9";
}
.fa-eercast:before {
  content: "\f2da";
}
.fa-microchip:before {
  content: "\f2db";
}
.fa-snowflake-o:before {
  content: "\f2dc";
}
.fa-superpowers:before {
  content: "\f2dd";
}
.fa-wpexplorer:before {
  content: "\f2de";
}
.fa-meetup:before {
  content: "\f2e0";
}
.sr-only {
  position: absolute;
  width: 1px;
  height: 1px;
  padding: 0;
  margin: -1px;
  overflow: hidden;
  clip: rect(0, 0, 0, 0);
  border: 0;
}
.sr-only-focusable:active,
.sr-only-focusable:focus {
  position: static;
  width: auto;
  height: auto;
  margin: 0;
  overflow: visible;
  clip: auto;
}
.sr-only-focusable:active,
.sr-only-focusable:focus {
  position: static;
  width: auto;
  height: auto;
  margin: 0;
  overflow: visible;
  clip: auto;
}
/*!
*
* IPython base
*
*/
.modal.fade .modal-dialog {
  -webkit-transform: translate(0, 0);
  -ms-transform: translate(0, 0);
  -o-transform: translate(0, 0);
  transform: translate(0, 0);
}
code {
  color: #000;
}
pre {
  font-size: inherit;
  line-height: inherit;
}
label {
  font-weight: normal;
}
/* Make the page background atleast 100% the height of the view port */
/* Make the page itself atleast 70% the height of the view port */
.border-box-sizing {
  box-sizing: border-box;
  -moz-box-sizing: border-box;
  -webkit-box-sizing: border-box;
}
.corner-all {
  border-radius: 2px;
}
.no-padding {
  padding: 0px;
}
/* Flexible box model classes */
/* Taken from Alex Russell http://infrequently.org/2009/08/css-3-progress/ */
/* This file is a compatability layer.  It allows the usage of flexible box 
model layouts accross multiple browsers, including older browsers.  The newest,
universal implementation of the flexible box model is used when available (see
`Modern browsers` comments below).  Browsers that are known to implement this 
new spec completely include:

    Firefox 28.0+
    Chrome 29.0+
    Internet Explorer 11+ 
    Opera 17.0+

Browsers not listed, including Safari, are supported via the styling under the
`Old browsers` comments below.
*/
.hbox {
  /* Old browsers */
  display: -webkit-box;
  -webkit-box-orient: horizontal;
  -webkit-box-align: stretch;
  display: -moz-box;
  -moz-box-orient: horizontal;
  -moz-box-align: stretch;
  display: box;
  box-orient: horizontal;
  box-align: stretch;
  /* Modern browsers */
  display: flex;
  flex-direction: row;
  align-items: stretch;
}
.hbox > * {
  /* Old browsers */
  -webkit-box-flex: 0;
  -moz-box-flex: 0;
  box-flex: 0;
  /* Modern browsers */
  flex: none;
}
.vbox {
  /* Old browsers */
  display: -webkit-box;
  -webkit-box-orient: vertical;
  -webkit-box-align: stretch;
  display: -moz-box;
  -moz-box-orient: vertical;
  -moz-box-align: stretch;
  display: box;
  box-orient: vertical;
  box-align: stretch;
  /* Modern browsers */
  display: flex;
  flex-direction: column;
  align-items: stretch;
}
.vbox > * {
  /* Old browsers */
  -webkit-box-flex: 0;
  -moz-box-flex: 0;
  box-flex: 0;
  /* Modern browsers */
  flex: none;
}
.hbox.reverse,
.vbox.reverse,
.reverse {
  /* Old browsers */
  -webkit-box-direction: reverse;
  -moz-box-direction: reverse;
  box-direction: reverse;
  /* Modern browsers */
  flex-direction: row-reverse;
}
.hbox.box-flex0,
.vbox.box-flex0,
.box-flex0 {
  /* Old browsers */
  -webkit-box-flex: 0;
  -moz-box-flex: 0;
  box-flex: 0;
  /* Modern browsers */
  flex: none;
  width: auto;
}
.hbox.box-flex1,
.vbox.box-flex1,
.box-flex1 {
  /* Old browsers */
  -webkit-box-flex: 1;
  -moz-box-flex: 1;
  box-flex: 1;
  /* Modern browsers */
  flex: 1;
}
.hbox.box-flex,
.vbox.box-flex,
.box-flex {
  /* Old browsers */
  /* Old browsers */
  -webkit-box-flex: 1;
  -moz-box-flex: 1;
  box-flex: 1;
  /* Modern browsers */
  flex: 1;
}
.hbox.box-flex2,
.vbox.box-flex2,
.box-flex2 {
  /* Old browsers */
  -webkit-box-flex: 2;
  -moz-box-flex: 2;
  box-flex: 2;
  /* Modern browsers */
  flex: 2;
}
.box-group1 {
  /*  Deprecated */
  -webkit-box-flex-group: 1;
  -moz-box-flex-group: 1;
  box-flex-group: 1;
}
.box-group2 {
  /* Deprecated */
  -webkit-box-flex-group: 2;
  -moz-box-flex-group: 2;
  box-flex-group: 2;
}
.hbox.start,
.vbox.start,
.start {
  /* Old browsers */
  -webkit-box-pack: start;
  -moz-box-pack: start;
  box-pack: start;
  /* Modern browsers */
  justify-content: flex-start;
}
.hbox.end,
.vbox.end,
.end {
  /* Old browsers */
  -webkit-box-pack: end;
  -moz-box-pack: end;
  box-pack: end;
  /* Modern browsers */
  justify-content: flex-end;
}
.hbox.center,
.vbox.center,
.center {
  /* Old browsers */
  -webkit-box-pack: center;
  -moz-box-pack: center;
  box-pack: center;
  /* Modern browsers */
  justify-content: center;
}
.hbox.baseline,
.vbox.baseline,
.baseline {
  /* Old browsers */
  -webkit-box-pack: baseline;
  -moz-box-pack: baseline;
  box-pack: baseline;
  /* Modern browsers */
  justify-content: baseline;
}
.hbox.stretch,
.vbox.stretch,
.stretch {
  /* Old browsers */
  -webkit-box-pack: stretch;
  -moz-box-pack: stretch;
  box-pack: stretch;
  /* Modern browsers */
  justify-content: stretch;
}
.hbox.align-start,
.vbox.align-start,
.align-start {
  /* Old browsers */
  -webkit-box-align: start;
  -moz-box-align: start;
  box-align: start;
  /* Modern browsers */
  align-items: flex-start;
}
.hbox.align-end,
.vbox.align-end,
.align-end {
  /* Old browsers */
  -webkit-box-align: end;
  -moz-box-align: end;
  box-align: end;
  /* Modern browsers */
  align-items: flex-end;
}
.hbox.align-center,
.vbox.align-center,
.align-center {
  /* Old browsers */
  -webkit-box-align: center;
  -moz-box-align: center;
  box-align: center;
  /* Modern browsers */
  align-items: center;
}
.hbox.align-baseline,
.vbox.align-baseline,
.align-baseline {
  /* Old browsers */
  -webkit-box-align: baseline;
  -moz-box-align: baseline;
  box-align: baseline;
  /* Modern browsers */
  align-items: baseline;
}
.hbox.align-stretch,
.vbox.align-stretch,
.align-stretch {
  /* Old browsers */
  -webkit-box-align: stretch;
  -moz-box-align: stretch;
  box-align: stretch;
  /* Modern browsers */
  align-items: stretch;
}
div.error {
  margin: 2em;
  text-align: center;
}
div.error > h1 {
  font-size: 500%;
  line-height: normal;
}
div.error > p {
  font-size: 200%;
  line-height: normal;
}
div.traceback-wrapper {
  text-align: left;
  max-width: 800px;
  margin: auto;
}
div.traceback-wrapper pre.traceback {
  max-height: 600px;
  overflow: auto;
}
/**
 * Primary styles
 *
 * Author: Jupyter Development Team
 */
body {
  background-color: #fff;
  /* This makes sure that the body covers the entire window and needs to
       be in a different element than the display: box in wrapper below */
  position: absolute;
  left: 0px;
  right: 0px;
  top: 0px;
  bottom: 0px;
  overflow: visible;
}
body > #header {
  /* Initially hidden to prevent FLOUC */
  display: none;
  background-color: #fff;
  /* Display over codemirror */
  position: relative;
  z-index: 100;
}
body > #header #header-container {
  display: flex;
  flex-direction: row;
  justify-content: space-between;
  padding: 5px;
  padding-bottom: 5px;
  padding-top: 5px;
  box-sizing: border-box;
  -moz-box-sizing: border-box;
  -webkit-box-sizing: border-box;
}
body > #header .header-bar {
  width: 100%;
  height: 1px;
  background: #e7e7e7;
  margin-bottom: -1px;
}
@media print {
  body > #header {
    display: none !important;
  }
}
#header-spacer {
  width: 100%;
  visibility: hidden;
}
@media print {
  #header-spacer {
    display: none;
  }
}
#ipython_notebook {
  padding-left: 0px;
  padding-top: 1px;
  padding-bottom: 1px;
}
[dir="rtl"] #ipython_notebook {
  margin-right: 10px;
  margin-left: 0;
}
[dir="rtl"] #ipython_notebook.pull-left {
  float: right !important;
  float: right;
}
.flex-spacer {
  flex: 1;
}
#noscript {
  width: auto;
  padding-top: 16px;
  padding-bottom: 16px;
  text-align: center;
  font-size: 22px;
  color: red;
  font-weight: bold;
}
#ipython_notebook img {
  height: 28px;
}
#site {
  width: 100%;
  display: none;
  box-sizing: border-box;
  -moz-box-sizing: border-box;
  -webkit-box-sizing: border-box;
  overflow: auto;
}
@media print {
  #site {
    height: auto !important;
  }
}
/* Smaller buttons */
.ui-button .ui-button-text {
  padding: 0.2em 0.8em;
  font-size: 77%;
}
input.ui-button {
  padding: 0.3em 0.9em;
}
span#kernel_logo_widget {
  margin: 0 10px;
}
span#login_widget {
  float: right;
}
[dir="rtl"] span#login_widget {
  float: left;
}
span#login_widget > .button,
#logout {
  color: #333;
  background-color: #fff;
  border-color: #ccc;
}
span#login_widget > .button:focus,
#logout:focus,
span#login_widget > .button.focus,
#logout.focus {
  color: #333;
  background-color: #e6e6e6;
  border-color: #8c8c8c;
}
span#login_widget > .button:hover,
#logout:hover {
  color: #333;
  background-color: #e6e6e6;
  border-color: #adadad;
}
span#login_widget > .button:active,
#logout:active,
span#login_widget > .button.active,
#logout.active,
.open > .dropdown-togglespan#login_widget > .button,
.open > .dropdown-toggle#logout {
  color: #333;
  background-color: #e6e6e6;
  border-color: #adadad;
}
span#login_widget > .button:active:hover,
#logout:active:hover,
span#login_widget > .button.active:hover,
#logout.active:hover,
.open > .dropdown-togglespan#login_widget > .button:hover,
.open > .dropdown-toggle#logout:hover,
span#login_widget > .button:active:focus,
#logout:active:focus,
span#login_widget > .button.active:focus,
#logout.active:focus,
.open > .dropdown-togglespan#login_widget > .button:focus,
.open > .dropdown-toggle#logout:focus,
span#login_widget > .button:active.focus,
#logout:active.focus,
span#login_widget > .button.active.focus,
#logout.active.focus,
.open > .dropdown-togglespan#login_widget > .button.focus,
.open > .dropdown-toggle#logout.focus {
  color: #333;
  background-color: #d4d4d4;
  border-color: #8c8c8c;
}
span#login_widget > .button:active,
#logout:active,
span#login_widget > .button.active,
#logout.active,
.open > .dropdown-togglespan#login_widget > .button,
.open > .dropdown-toggle#logout {
  background-image: none;
}
span#login_widget > .button.disabled:hover,
#logout.disabled:hover,
span#login_widget > .button[disabled]:hover,
#logout[disabled]:hover,
fieldset[disabled] span#login_widget > .button:hover,
fieldset[disabled] #logout:hover,
span#login_widget > .button.disabled:focus,
#logout.disabled:focus,
span#login_widget > .button[disabled]:focus,
#logout[disabled]:focus,
fieldset[disabled] span#login_widget > .button:focus,
fieldset[disabled] #logout:focus,
span#login_widget > .button.disabled.focus,
#logout.disabled.focus,
span#login_widget > .button[disabled].focus,
#logout[disabled].focus,
fieldset[disabled] span#login_widget > .button.focus,
fieldset[disabled] #logout.focus {
  background-color: #fff;
  border-color: #ccc;
}
span#login_widget > .button .badge,
#logout .badge {
  color: #fff;
  background-color: #333;
}
.nav-header {
  text-transform: none;
}
#header > span {
  margin-top: 10px;
}
.modal_stretch .modal-dialog {
  /* Old browsers */
  display: -webkit-box;
  -webkit-box-orient: vertical;
  -webkit-box-align: stretch;
  display: -moz-box;
  -moz-box-orient: vertical;
  -moz-box-align: stretch;
  display: box;
  box-orient: vertical;
  box-align: stretch;
  /* Modern browsers */
  display: flex;
  flex-direction: column;
  align-items: stretch;
  min-height: 80vh;
}
.modal_stretch .modal-dialog .modal-body {
  max-height: calc(100vh - 200px);
  overflow: auto;
  flex: 1;
}
.modal-header {
  cursor: move;
}
@media (min-width: 768px) {
  .modal .modal-dialog {
    width: 700px;
  }
}
@media (min-width: 768px) {
  select.form-control {
    margin-left: 12px;
    margin-right: 12px;
  }
}
/*!
*
* IPython auth
*
*/
.center-nav {
  display: inline-block;
  margin-bottom: -4px;
}
[dir="rtl"] .center-nav form.pull-left {
  float: right !important;
  float: right;
}
[dir="rtl"] .center-nav .navbar-text {
  float: right;
}
[dir="rtl"] .navbar-inner {
  text-align: right;
}
[dir="rtl"] div.text-left {
  text-align: right;
}
/*!
*
* IPython tree view
*
*/
/* We need an invisible input field on top of the sentense*/
/* "Drag file onto the list ..." */
.alternate_upload {
  background-color: none;
  display: inline;
}
.alternate_upload.form {
  padding: 0;
  margin: 0;
}
.alternate_upload input.fileinput {
  position: absolute;
  display: block;
  width: 100%;
  height: 100%;
  overflow: hidden;
  cursor: pointer;
  opacity: 0;
  z-index: 2;
}
.alternate_upload .btn-xs > input.fileinput {
  margin: -1px -5px;
}
.alternate_upload .btn-upload {
  position: relative;
  height: 22px;
}
::-webkit-file-upload-button {
  cursor: pointer;
}
/**
 * Primary styles
 *
 * Author: Jupyter Development Team
 */
ul#tabs {
  margin-bottom: 4px;
}
ul#tabs a {
  padding-top: 6px;
  padding-bottom: 4px;
}
[dir="rtl"] ul#tabs.nav-tabs > li {
  float: right;
}
[dir="rtl"] ul#tabs.nav.nav-tabs {
  padding-right: 0;
}
ul.breadcrumb a:focus,
ul.breadcrumb a:hover {
  text-decoration: none;
}
ul.breadcrumb i.icon-home {
  font-size: 16px;
  margin-right: 4px;
}
ul.breadcrumb span {
  color: #5e5e5e;
}
.list_toolbar {
  padding: 4px 0 4px 0;
  vertical-align: middle;
}
.list_toolbar .tree-buttons {
  padding-top: 1px;
}
[dir="rtl"] .list_toolbar .tree-buttons .pull-right {
  float: left !important;
  float: left;
}
[dir="rtl"] .list_toolbar .col-sm-4,
[dir="rtl"] .list_toolbar .col-sm-8 {
  float: right;
}
.dynamic-buttons {
  padding-top: 3px;
  display: inline-block;
}
.list_toolbar [class*="span"] {
  min-height: 24px;
}
.list_header {
  font-weight: bold;
  background-color: #EEE;
}
.list_placeholder {
  font-weight: bold;
  padding-top: 4px;
  padding-bottom: 4px;
  padding-left: 7px;
  padding-right: 7px;
}
.list_container {
  margin-top: 4px;
  margin-bottom: 20px;
  border: 1px solid #ddd;
  border-radius: 2px;
}
.list_container > div {
  border-bottom: 1px solid #ddd;
}
.list_container > div:hover .list-item {
  background-color: red;
}
.list_container > div:last-child {
  border: none;
}
.list_item:hover .list_item {
  background-color: #ddd;
}
.list_item a {
  text-decoration: none;
}
.list_item:hover {
  background-color: #fafafa;
}
.list_header > div,
.list_item > div {
  padding-top: 4px;
  padding-bottom: 4px;
  padding-left: 7px;
  padding-right: 7px;
  line-height: 22px;
}
.list_header > div input,
.list_item > div input {
  margin-right: 7px;
  margin-left: 14px;
  vertical-align: text-bottom;
  line-height: 22px;
  position: relative;
  top: -1px;
}
.list_header > div .item_link,
.list_item > div .item_link {
  margin-left: -1px;
  vertical-align: baseline;
  line-height: 22px;
}
[dir="rtl"] .list_item > div input {
  margin-right: 0;
}
.new-file input[type=checkbox] {
  visibility: hidden;
}
.item_name {
  line-height: 22px;
  height: 24px;
}
.item_icon {
  font-size: 14px;
  color: #5e5e5e;
  margin-right: 7px;
  margin-left: 7px;
  line-height: 22px;
  vertical-align: baseline;
}
.item_modified {
  margin-right: 7px;
  margin-left: 7px;
}
[dir="rtl"] .item_modified.pull-right {
  float: left !important;
  float: left;
}
.item_buttons {
  line-height: 1em;
  margin-left: -5px;
}
.item_buttons .btn,
.item_buttons .btn-group,
.item_buttons .input-group {
  float: left;
}
.item_buttons > .btn,
.item_buttons > .btn-group,
.item_buttons > .input-group {
  margin-left: 5px;
}
.item_buttons .btn {
  min-width: 13ex;
}
.item_buttons .running-indicator {
  padding-top: 4px;
  color: #5cb85c;
}
.item_buttons .kernel-name {
  padding-top: 4px;
  color: #5bc0de;
  margin-right: 7px;
  float: left;
}
[dir="rtl"] .item_buttons.pull-right {
  float: left !important;
  float: left;
}
[dir="rtl"] .item_buttons .kernel-name {
  margin-left: 7px;
  float: right;
}
.toolbar_info {
  height: 24px;
  line-height: 24px;
}
.list_item input:not([type=checkbox]) {
  padding-top: 3px;
  padding-bottom: 3px;
  height: 22px;
  line-height: 14px;
  margin: 0px;
}
.highlight_text {
  color: blue;
}
#project_name {
  display: inline-block;
  padding-left: 7px;
  margin-left: -2px;
}
#project_name > .breadcrumb {
  padding: 0px;
  margin-bottom: 0px;
  background-color: transparent;
  font-weight: bold;
}
.sort_button {
  display: inline-block;
  padding-left: 7px;
}
[dir="rtl"] .sort_button.pull-right {
  float: left !important;
  float: left;
}
#tree-selector {
  padding-right: 0px;
}
#button-select-all {
  min-width: 50px;
}
[dir="rtl"] #button-select-all.btn {
  float: right ;
}
#select-all {
  margin-left: 7px;
  margin-right: 2px;
  margin-top: 2px;
  height: 16px;
}
[dir="rtl"] #select-all.pull-left {
  float: right !important;
  float: right;
}
.menu_icon {
  margin-right: 2px;
}
.tab-content .row {
  margin-left: 0px;
  margin-right: 0px;
}
.folder_icon:before {
  display: inline-block;
  font: normal normal normal 14px/1 FontAwesome;
  font-size: inherit;
  text-rendering: auto;
  -webkit-font-smoothing: antialiased;
  -moz-osx-font-smoothing: grayscale;
  content: "\f114";
}
.folder_icon:before.fa-pull-left {
  margin-right: .3em;
}
.folder_icon:before.fa-pull-right {
  margin-left: .3em;
}
.folder_icon:before.pull-left {
  margin-right: .3em;
}
.folder_icon:before.pull-right {
  margin-left: .3em;
}
.notebook_icon:before {
  display: inline-block;
  font: normal normal normal 14px/1 FontAwesome;
  font-size: inherit;
  text-rendering: auto;
  -webkit-font-smoothing: antialiased;
  -moz-osx-font-smoothing: grayscale;
  content: "\f02d";
  position: relative;
  top: -1px;
}
.notebook_icon:before.fa-pull-left {
  margin-right: .3em;
}
.notebook_icon:before.fa-pull-right {
  margin-left: .3em;
}
.notebook_icon:before.pull-left {
  margin-right: .3em;
}
.notebook_icon:before.pull-right {
  margin-left: .3em;
}
.running_notebook_icon:before {
  display: inline-block;
  font: normal normal normal 14px/1 FontAwesome;
  font-size: inherit;
  text-rendering: auto;
  -webkit-font-smoothing: antialiased;
  -moz-osx-font-smoothing: grayscale;
  content: "\f02d";
  position: relative;
  top: -1px;
  color: #5cb85c;
}
.running_notebook_icon:before.fa-pull-left {
  margin-right: .3em;
}
.running_notebook_icon:before.fa-pull-right {
  margin-left: .3em;
}
.running_notebook_icon:before.pull-left {
  margin-right: .3em;
}
.running_notebook_icon:before.pull-right {
  margin-left: .3em;
}
.file_icon:before {
  display: inline-block;
  font: normal normal normal 14px/1 FontAwesome;
  font-size: inherit;
  text-rendering: auto;
  -webkit-font-smoothing: antialiased;
  -moz-osx-font-smoothing: grayscale;
  content: "\f016";
  position: relative;
  top: -2px;
}
.file_icon:before.fa-pull-left {
  margin-right: .3em;
}
.file_icon:before.fa-pull-right {
  margin-left: .3em;
}
.file_icon:before.pull-left {
  margin-right: .3em;
}
.file_icon:before.pull-right {
  margin-left: .3em;
}
#notebook_toolbar .pull-right {
  padding-top: 0px;
  margin-right: -1px;
}
ul#new-menu {
  left: auto;
  right: 0;
}
#new-menu .dropdown-header {
  font-size: 10px;
  border-bottom: 1px solid #e5e5e5;
  padding: 0 0 3px;
  margin: -3px 20px 0;
}
.kernel-menu-icon {
  padding-right: 12px;
  width: 24px;
  content: "\f096";
}
.kernel-menu-icon:before {
  content: "\f096";
}
.kernel-menu-icon-current:before {
  content: "\f00c";
}
#tab_content {
  padding-top: 20px;
}
#running .panel-group .panel {
  margin-top: 3px;
  margin-bottom: 1em;
}
#running .panel-group .panel .panel-heading {
  background-color: #EEE;
  padding-top: 4px;
  padding-bottom: 4px;
  padding-left: 7px;
  padding-right: 7px;
  line-height: 22px;
}
#running .panel-group .panel .panel-heading a:focus,
#running .panel-group .panel .panel-heading a:hover {
  text-decoration: none;
}
#running .panel-group .panel .panel-body {
  padding: 0px;
}
#running .panel-group .panel .panel-body .list_container {
  margin-top: 0px;
  margin-bottom: 0px;
  border: 0px;
  border-radius: 0px;
}
#running .panel-group .panel .panel-body .list_container .list_item {
  border-bottom: 1px solid #ddd;
}
#running .panel-group .panel .panel-body .list_container .list_item:last-child {
  border-bottom: 0px;
}
.delete-button {
  display: none;
}
.duplicate-button {
  display: none;
}
.rename-button {
  display: none;
}
.move-button {
  display: none;
}
.download-button {
  display: none;
}
.shutdown-button {
  display: none;
}
.dynamic-instructions {
  display: inline-block;
  padding-top: 4px;
}
/*!
*
* IPython text editor webapp
*
*/
.selected-keymap i.fa {
  padding: 0px 5px;
}
.selected-keymap i.fa:before {
  content: "\f00c";
}
#mode-menu {
  overflow: auto;
  max-height: 20em;
}
.edit_app #header {
  -webkit-box-shadow: 0px 0px 12px 1px rgba(87, 87, 87, 0.2);
  box-shadow: 0px 0px 12px 1px rgba(87, 87, 87, 0.2);
}
.edit_app #menubar .navbar {
  /* Use a negative 1 bottom margin, so the border overlaps the border of the
    header */
  margin-bottom: -1px;
}
.dirty-indicator {
  display: inline-block;
  font: normal normal normal 14px/1 FontAwesome;
  font-size: inherit;
  text-rendering: auto;
  -webkit-font-smoothing: antialiased;
  -moz-osx-font-smoothing: grayscale;
  width: 20px;
}
.dirty-indicator.fa-pull-left {
  margin-right: .3em;
}
.dirty-indicator.fa-pull-right {
  margin-left: .3em;
}
.dirty-indicator.pull-left {
  margin-right: .3em;
}
.dirty-indicator.pull-right {
  margin-left: .3em;
}
.dirty-indicator-dirty {
  display: inline-block;
  font: normal normal normal 14px/1 FontAwesome;
  font-size: inherit;
  text-rendering: auto;
  -webkit-font-smoothing: antialiased;
  -moz-osx-font-smoothing: grayscale;
  width: 20px;
}
.dirty-indicator-dirty.fa-pull-left {
  margin-right: .3em;
}
.dirty-indicator-dirty.fa-pull-right {
  margin-left: .3em;
}
.dirty-indicator-dirty.pull-left {
  margin-right: .3em;
}
.dirty-indicator-dirty.pull-right {
  margin-left: .3em;
}
.dirty-indicator-clean {
  display: inline-block;
  font: normal normal normal 14px/1 FontAwesome;
  font-size: inherit;
  text-rendering: auto;
  -webkit-font-smoothing: antialiased;
  -moz-osx-font-smoothing: grayscale;
  width: 20px;
}
.dirty-indicator-clean.fa-pull-left {
  margin-right: .3em;
}
.dirty-indicator-clean.fa-pull-right {
  margin-left: .3em;
}
.dirty-indicator-clean.pull-left {
  margin-right: .3em;
}
.dirty-indicator-clean.pull-right {
  margin-left: .3em;
}
.dirty-indicator-clean:before {
  display: inline-block;
  font: normal normal normal 14px/1 FontAwesome;
  font-size: inherit;
  text-rendering: auto;
  -webkit-font-smoothing: antialiased;
  -moz-osx-font-smoothing: grayscale;
  content: "\f00c";
}
.dirty-indicator-clean:before.fa-pull-left {
  margin-right: .3em;
}
.dirty-indicator-clean:before.fa-pull-right {
  margin-left: .3em;
}
.dirty-indicator-clean:before.pull-left {
  margin-right: .3em;
}
.dirty-indicator-clean:before.pull-right {
  margin-left: .3em;
}
#filename {
  font-size: 16pt;
  display: table;
  padding: 0px 5px;
}
#current-mode {
  padding-left: 5px;
  padding-right: 5px;
}
#texteditor-backdrop {
  padding-top: 20px;
  padding-bottom: 20px;
}
@media not print {
  #texteditor-backdrop {
    background-color: #EEE;
  }
}
@media print {
  #texteditor-backdrop #texteditor-container .CodeMirror-gutter,
  #texteditor-backdrop #texteditor-container .CodeMirror-gutters {
    background-color: #fff;
  }
}
@media not print {
  #texteditor-backdrop #texteditor-container .CodeMirror-gutter,
  #texteditor-backdrop #texteditor-container .CodeMirror-gutters {
    background-color: #fff;
  }
}
@media not print {
  #texteditor-backdrop #texteditor-container {
    padding: 0px;
    background-color: #fff;
    -webkit-box-shadow: 0px 0px 12px 1px rgba(87, 87, 87, 0.2);
    box-shadow: 0px 0px 12px 1px rgba(87, 87, 87, 0.2);
  }
}
.CodeMirror-dialog {
  background-color: #fff;
}
/*!
*
* IPython notebook
*
*/
/* CSS font colors for translated ANSI escape sequences */
/* The color values are a mix of
   http://www.xcolors.net/dl/baskerville-ivorylight and
   http://www.xcolors.net/dl/euphrasia */
.ansi-black-fg {
  color: #3E424D;
}
.ansi-black-bg {
  background-color: #3E424D;
}
.ansi-black-intense-fg {
  color: #282C36;
}
.ansi-black-intense-bg {
  background-color: #282C36;
}
.ansi-red-fg {
  color: #E75C58;
}
.ansi-red-bg {
  background-color: #E75C58;
}
.ansi-red-intense-fg {
  color: #B22B31;
}
.ansi-red-intense-bg {
  background-color: #B22B31;
}
.ansi-green-fg {
  color: #00A250;
}
.ansi-green-bg {
  background-color: #00A250;
}
.ansi-green-intense-fg {
  color: #007427;
}
.ansi-green-intense-bg {
  background-color: #007427;
}
.ansi-yellow-fg {
  color: #DDB62B;
}
.ansi-yellow-bg {
  background-color: #DDB62B;
}
.ansi-yellow-intense-fg {
  color: #B27D12;
}
.ansi-yellow-intense-bg {
  background-color: #B27D12;
}
.ansi-blue-fg {
  color: #208FFB;
}
.ansi-blue-bg {
  background-color: #208FFB;
}
.ansi-blue-intense-fg {
  color: #0065CA;
}
.ansi-blue-intense-bg {
  background-color: #0065CA;
}
.ansi-magenta-fg {
  color: #D160C4;
}
.ansi-magenta-bg {
  background-color: #D160C4;
}
.ansi-magenta-intense-fg {
  color: #A03196;
}
.ansi-magenta-intense-bg {
  background-color: #A03196;
}
.ansi-cyan-fg {
  color: #60C6C8;
}
.ansi-cyan-bg {
  background-color: #60C6C8;
}
.ansi-cyan-intense-fg {
  color: #258F8F;
}
.ansi-cyan-intense-bg {
  background-color: #258F8F;
}
.ansi-white-fg {
  color: #C5C1B4;
}
.ansi-white-bg {
  background-color: #C5C1B4;
}
.ansi-white-intense-fg {
  color: #A1A6B2;
}
.ansi-white-intense-bg {
  background-color: #A1A6B2;
}
.ansi-default-inverse-fg {
  color: #FFFFFF;
}
.ansi-default-inverse-bg {
  background-color: #000000;
}
.ansi-bold {
  font-weight: bold;
}
.ansi-underline {
  text-decoration: underline;
}
/* The following styles are deprecated an will be removed in a future version */
.ansibold {
  font-weight: bold;
}
.ansi-inverse {
  outline: 0.5px dotted;
}
/* use dark versions for foreground, to improve visibility */
.ansiblack {
  color: black;
}
.ansired {
  color: darkred;
}
.ansigreen {
  color: darkgreen;
}
.ansiyellow {
  color: #c4a000;
}
.ansiblue {
  color: darkblue;
}
.ansipurple {
  color: darkviolet;
}
.ansicyan {
  color: steelblue;
}
.ansigray {
  color: gray;
}
/* and light for background, for the same reason */
.ansibgblack {
  background-color: black;
}
.ansibgred {
  background-color: red;
}
.ansibggreen {
  background-color: green;
}
.ansibgyellow {
  background-color: yellow;
}
.ansibgblue {
  background-color: blue;
}
.ansibgpurple {
  background-color: magenta;
}
.ansibgcyan {
  background-color: cyan;
}
.ansibggray {
  background-color: gray;
}
div.cell {
  /* Old browsers */
  display: -webkit-box;
  -webkit-box-orient: vertical;
  -webkit-box-align: stretch;
  display: -moz-box;
  -moz-box-orient: vertical;
  -moz-box-align: stretch;
  display: box;
  box-orient: vertical;
  box-align: stretch;
  /* Modern browsers */
  display: flex;
  flex-direction: column;
  align-items: stretch;
  border-radius: 2px;
  box-sizing: border-box;
  -moz-box-sizing: border-box;
  -webkit-box-sizing: border-box;
  border-width: 1px;
  border-style: solid;
  border-color: transparent;
  width: 100%;
  padding: 5px;
  /* This acts as a spacer between cells, that is outside the border */
  margin: 0px;
  outline: none;
  position: relative;
  overflow: visible;
}
div.cell:before {
  position: absolute;
  display: block;
  top: -1px;
  left: -1px;
  width: 5px;
  height: calc(100% +  2px);
  content: '';
  background: transparent;
}
div.cell.jupyter-soft-selected {
  border-left-color: #E3F2FD;
  border-left-width: 1px;
  padding-left: 5px;
  border-right-color: #E3F2FD;
  border-right-width: 1px;
  background: #E3F2FD;
}
@media print {
  div.cell.jupyter-soft-selected {
    border-color: transparent;
  }
}
div.cell.selected,
div.cell.selected.jupyter-soft-selected {
  border-color: #ababab;
}
div.cell.selected:before,
div.cell.selected.jupyter-soft-selected:before {
  position: absolute;
  display: block;
  top: -1px;
  left: -1px;
  width: 5px;
  height: calc(100% +  2px);
  content: '';
  background: #42A5F5;
}
@media print {
  div.cell.selected,
  div.cell.selected.jupyter-soft-selected {
    border-color: transparent;
  }
}
.edit_mode div.cell.selected {
  border-color: #66BB6A;
}
.edit_mode div.cell.selected:before {
  position: absolute;
  display: block;
  top: -1px;
  left: -1px;
  width: 5px;
  height: calc(100% +  2px);
  content: '';
  background: #66BB6A;
}
@media print {
  .edit_mode div.cell.selected {
    border-color: transparent;
  }
}
.prompt {
  /* This needs to be wide enough for 3 digit prompt numbers: In[100]: */
  min-width: 14ex;
  /* This padding is tuned to match the padding on the CodeMirror editor. */
  padding: 0.4em;
  margin: 0px;
  font-family: monospace;
  text-align: right;
  /* This has to match that of the the CodeMirror class line-height below */
  line-height: 1.21429em;
  /* Don't highlight prompt number selection */
  -webkit-touch-callout: none;
  -webkit-user-select: none;
  -khtml-user-select: none;
  -moz-user-select: none;
  -ms-user-select: none;
  user-select: none;
  /* Use default cursor */
  cursor: default;
}
@media (max-width: 540px) {
  .prompt {
    text-align: left;
  }
}
div.inner_cell {
  min-width: 0;
  /* Old browsers */
  display: -webkit-box;
  -webkit-box-orient: vertical;
  -webkit-box-align: stretch;
  display: -moz-box;
  -moz-box-orient: vertical;
  -moz-box-align: stretch;
  display: box;
  box-orient: vertical;
  box-align: stretch;
  /* Modern browsers */
  display: flex;
  flex-direction: column;
  align-items: stretch;
  /* Old browsers */
  -webkit-box-flex: 1;
  -moz-box-flex: 1;
  box-flex: 1;
  /* Modern browsers */
  flex: 1;
}
/* input_area and input_prompt must match in top border and margin for alignment */
div.input_area {
  border: 1px solid #cfcfcf;
  border-radius: 2px;
  background: #f7f7f7;
  line-height: 1.21429em;
}
/* This is needed so that empty prompt areas can collapse to zero height when there
   is no content in the output_subarea and the prompt. The main purpose of this is
   to make sure that empty JavaScript output_subareas have no height. */
div.prompt:empty {
  padding-top: 0;
  padding-bottom: 0;
}
div.unrecognized_cell {
  padding: 5px 5px 5px 0px;
  /* Old browsers */
  display: -webkit-box;
  -webkit-box-orient: horizontal;
  -webkit-box-align: stretch;
  display: -moz-box;
  -moz-box-orient: horizontal;
  -moz-box-align: stretch;
  display: box;
  box-orient: horizontal;
  box-align: stretch;
  /* Modern browsers */
  display: flex;
  flex-direction: row;
  align-items: stretch;
}
div.unrecognized_cell .inner_cell {
  border-radius: 2px;
  padding: 5px;
  font-weight: bold;
  color: red;
  border: 1px solid #cfcfcf;
  background: #eaeaea;
}
div.unrecognized_cell .inner_cell a {
  color: inherit;
  text-decoration: none;
}
div.unrecognized_cell .inner_cell a:hover {
  color: inherit;
  text-decoration: none;
}
@media (max-width: 540px) {
  div.unrecognized_cell > div.prompt {
    display: none;
  }
}
div.code_cell {
  /* avoid page breaking on code cells when printing */
}
@media print {
  div.code_cell {
    page-break-inside: avoid;
  }
}
/* any special styling for code cells that are currently running goes here */
div.input {
  page-break-inside: avoid;
  /* Old browsers */
  display: -webkit-box;
  -webkit-box-orient: horizontal;
  -webkit-box-align: stretch;
  display: -moz-box;
  -moz-box-orient: horizontal;
  -moz-box-align: stretch;
  display: box;
  box-orient: horizontal;
  box-align: stretch;
  /* Modern browsers */
  display: flex;
  flex-direction: row;
  align-items: stretch;
}
@media (max-width: 540px) {
  div.input {
    /* Old browsers */
    display: -webkit-box;
    -webkit-box-orient: vertical;
    -webkit-box-align: stretch;
    display: -moz-box;
    -moz-box-orient: vertical;
    -moz-box-align: stretch;
    display: box;
    box-orient: vertical;
    box-align: stretch;
    /* Modern browsers */
    display: flex;
    flex-direction: column;
    align-items: stretch;
  }
}
/* input_area and input_prompt must match in top border and margin for alignment */
div.input_prompt {
  color: #303F9F;
  border-top: 1px solid transparent;
}
div.input_area > div.highlight {
  margin: 0.4em;
  border: none;
  padding: 0px;
  background-color: transparent;
}
div.input_area > div.highlight > pre {
  margin: 0px;
  border: none;
  padding: 0px;
  background-color: transparent;
}
/* The following gets added to the <head> if it is detected that the user has a
 * monospace font with inconsistent normal/bold/italic height.  See
 * notebookmain.js.  Such fonts will have keywords vertically offset with
 * respect to the rest of the text.  The user should select a better font.
 * See: https://github.com/ipython/ipython/issues/1503
 *
 * .CodeMirror span {
 *      vertical-align: bottom;
 * }
 */
.CodeMirror {
  line-height: 1.21429em;
  /* Changed from 1em to our global default */
  font-size: 14px;
  height: auto;
  /* Changed to auto to autogrow */
  background: none;
  /* Changed from white to allow our bg to show through */
}
.CodeMirror-scroll {
  /*  The CodeMirror docs are a bit fuzzy on if overflow-y should be hidden or visible.*/
  /*  We have found that if it is visible, vertical scrollbars appear with font size changes.*/
  overflow-y: hidden;
  overflow-x: auto;
}
.CodeMirror-lines {
  /* In CM2, this used to be 0.4em, but in CM3 it went to 4px. We need the em value because */
  /* we have set a different line-height and want this to scale with that. */
  /* Note that this should set vertical padding only, since CodeMirror assumes
       that horizontal padding will be set on CodeMirror pre */
  padding: 0.4em 0;
}
.CodeMirror-linenumber {
  padding: 0 8px 0 4px;
}
.CodeMirror-gutters {
  border-bottom-left-radius: 2px;
  border-top-left-radius: 2px;
}
.CodeMirror pre {
  /* In CM3 this went to 4px from 0 in CM2. This sets horizontal padding only,
    use .CodeMirror-lines for vertical */
  padding: 0 0.4em;
  border: 0;
  border-radius: 0;
}
.CodeMirror-cursor {
  border-left: 1.4px solid black;
}
@media screen and (min-width: 2138px) and (max-width: 4319px) {
  .CodeMirror-cursor {
    border-left: 2px solid black;
  }
}
@media screen and (min-width: 4320px) {
  .CodeMirror-cursor {
    border-left: 4px solid black;
  }
}
/*

Original style from softwaremaniacs.org (c) Ivan Sagalaev <Maniac@SoftwareManiacs.Org>
Adapted from GitHub theme

*/
.highlight-base {
  color: #000;
}
.highlight-variable {
  color: #000;
}
.highlight-variable-2 {
  color: #1a1a1a;
}
.highlight-variable-3 {
  color: #333333;
}
.highlight-string {
  color: #BA2121;
}
.highlight-comment {
  color: #408080;
  font-style: italic;
}
.highlight-number {
  color: #080;
}
.highlight-atom {
  color: #88F;
}
.highlight-keyword {
  color: #008000;
  font-weight: bold;
}
.highlight-builtin {
  color: #008000;
}
.highlight-error {
  color: #f00;
}
.highlight-operator {
  color: #AA22FF;
  font-weight: bold;
}
.highlight-meta {
  color: #AA22FF;
}
/* previously not defined, copying from default codemirror */
.highlight-def {
  color: #00f;
}
.highlight-string-2 {
  color: #f50;
}
.highlight-qualifier {
  color: #555;
}
.highlight-bracket {
  color: #997;
}
.highlight-tag {
  color: #170;
}
.highlight-attribute {
  color: #00c;
}
.highlight-header {
  color: blue;
}
.highlight-quote {
  color: #090;
}
.highlight-link {
  color: #00c;
}
/* apply the same style to codemirror */
.cm-s-ipython span.cm-keyword {
  color: #008000;
  font-weight: bold;
}
.cm-s-ipython span.cm-atom {
  color: #88F;
}
.cm-s-ipython span.cm-number {
  color: #080;
}
.cm-s-ipython span.cm-def {
  color: #00f;
}
.cm-s-ipython span.cm-variable {
  color: #000;
}
.cm-s-ipython span.cm-operator {
  color: #AA22FF;
  font-weight: bold;
}
.cm-s-ipython span.cm-variable-2 {
  color: #1a1a1a;
}
.cm-s-ipython span.cm-variable-3 {
  color: #333333;
}
.cm-s-ipython span.cm-comment {
  color: #408080;
  font-style: italic;
}
.cm-s-ipython span.cm-string {
  color: #BA2121;
}
.cm-s-ipython span.cm-string-2 {
  color: #f50;
}
.cm-s-ipython span.cm-meta {
  color: #AA22FF;
}
.cm-s-ipython span.cm-qualifier {
  color: #555;
}
.cm-s-ipython span.cm-builtin {
  color: #008000;
}
.cm-s-ipython span.cm-bracket {
  color: #997;
}
.cm-s-ipython span.cm-tag {
  color: #170;
}
.cm-s-ipython span.cm-attribute {
  color: #00c;
}
.cm-s-ipython span.cm-header {
  color: blue;
}
.cm-s-ipython span.cm-quote {
  color: #090;
}
.cm-s-ipython span.cm-link {
  color: #00c;
}
.cm-s-ipython span.cm-error {
  color: #f00;
}
.cm-s-ipython span.cm-tab {
  background: url(data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAADAAAAAMCAYAAAAkuj5RAAAAAXNSR0IArs4c6QAAAGFJREFUSMft1LsRQFAQheHPowAKoACx3IgEKtaEHujDjORSgWTH/ZOdnZOcM/sgk/kFFWY0qV8foQwS4MKBCS3qR6ixBJvElOobYAtivseIE120FaowJPN75GMu8j/LfMwNjh4HUpwg4LUAAAAASUVORK5CYII=);
  background-position: right;
  background-repeat: no-repeat;
}
div.output_wrapper {
  /* this position must be relative to enable descendents to be absolute within it */
  position: relative;
  /* Old browsers */
  display: -webkit-box;
  -webkit-box-orient: vertical;
  -webkit-box-align: stretch;
  display: -moz-box;
  -moz-box-orient: vertical;
  -moz-box-align: stretch;
  display: box;
  box-orient: vertical;
  box-align: stretch;
  /* Modern browsers */
  display: flex;
  flex-direction: column;
  align-items: stretch;
  z-index: 1;
}
/* class for the output area when it should be height-limited */
div.output_scroll {
  /* ideally, this would be max-height, but FF barfs all over that */
  height: 24em;
  /* FF needs this *and the wrapper* to specify full width, or it will shrinkwrap */
  width: 100%;
  overflow: auto;
  border-radius: 2px;
  -webkit-box-shadow: inset 0 2px 8px rgba(0, 0, 0, 0.8);
  box-shadow: inset 0 2px 8px rgba(0, 0, 0, 0.8);
  display: block;
}
/* output div while it is collapsed */
div.output_collapsed {
  margin: 0px;
  padding: 0px;
  /* Old browsers */
  display: -webkit-box;
  -webkit-box-orient: vertical;
  -webkit-box-align: stretch;
  display: -moz-box;
  -moz-box-orient: vertical;
  -moz-box-align: stretch;
  display: box;
  box-orient: vertical;
  box-align: stretch;
  /* Modern browsers */
  display: flex;
  flex-direction: column;
  align-items: stretch;
}
div.out_prompt_overlay {
  height: 100%;
  padding: 0px 0.4em;
  position: absolute;
  border-radius: 2px;
}
div.out_prompt_overlay:hover {
  /* use inner shadow to get border that is computed the same on WebKit/FF */
  -webkit-box-shadow: inset 0 0 1px #000;
  box-shadow: inset 0 0 1px #000;
  background: rgba(240, 240, 240, 0.5);
}
div.output_prompt {
  color: #D84315;
}
/* This class is the outer container of all output sections. */
div.output_area {
  padding: 0px;
  page-break-inside: avoid;
  /* Old browsers */
  display: -webkit-box;
  -webkit-box-orient: horizontal;
  -webkit-box-align: stretch;
  display: -moz-box;
  -moz-box-orient: horizontal;
  -moz-box-align: stretch;
  display: box;
  box-orient: horizontal;
  box-align: stretch;
  /* Modern browsers */
  display: flex;
  flex-direction: row;
  align-items: stretch;
}
div.output_area .MathJax_Display {
  text-align: left !important;
}
div.output_area .rendered_html table {
  margin-left: 0;
  margin-right: 0;
}
div.output_area .rendered_html img {
  margin-left: 0;
  margin-right: 0;
}
div.output_area img,
div.output_area svg {
  max-width: 100%;
  height: auto;
}
div.output_area img.unconfined,
div.output_area svg.unconfined {
  max-width: none;
}
div.output_area .mglyph > img {
  max-width: none;
}
/* This is needed to protect the pre formating from global settings such
   as that of bootstrap */
.output {
  /* Old browsers */
  display: -webkit-box;
  -webkit-box-orient: vertical;
  -webkit-box-align: stretch;
  display: -moz-box;
  -moz-box-orient: vertical;
  -moz-box-align: stretch;
  display: box;
  box-orient: vertical;
  box-align: stretch;
  /* Modern browsers */
  display: flex;
  flex-direction: column;
  align-items: stretch;
}
@media (max-width: 540px) {
  div.output_area {
    /* Old browsers */
    display: -webkit-box;
    -webkit-box-orient: vertical;
    -webkit-box-align: stretch;
    display: -moz-box;
    -moz-box-orient: vertical;
    -moz-box-align: stretch;
    display: box;
    box-orient: vertical;
    box-align: stretch;
    /* Modern browsers */
    display: flex;
    flex-direction: column;
    align-items: stretch;
  }
}
div.output_area pre {
  margin: 0;
  padding: 1px 0 1px 0;
  border: 0;
  vertical-align: baseline;
  color: black;
  background-color: transparent;
  border-radius: 0;
}
/* This class is for the output subarea inside the output_area and after
   the prompt div. */
div.output_subarea {
  overflow-x: auto;
  padding: 0.4em;
  /* Old browsers */
  -webkit-box-flex: 1;
  -moz-box-flex: 1;
  box-flex: 1;
  /* Modern browsers */
  flex: 1;
  max-width: calc(100% - 14ex);
}
div.output_scroll div.output_subarea {
  overflow-x: visible;
}
/* The rest of the output_* classes are for special styling of the different
   output types */
/* all text output has this class: */
div.output_text {
  text-align: left;
  color: #000;
  /* This has to match that of the the CodeMirror class line-height below */
  line-height: 1.21429em;
}
/* stdout/stderr are 'text' as well as 'stream', but execute_result/error are *not* streams */
div.output_stderr {
  background: #fdd;
  /* very light red background for stderr */
}
div.output_latex {
  text-align: left;
}
/* Empty output_javascript divs should have no height */
div.output_javascript:empty {
  padding: 0;
}
.js-error {
  color: darkred;
}
/* raw_input styles */
div.raw_input_container {
  line-height: 1.21429em;
  padding-top: 5px;
}
pre.raw_input_prompt {
  /* nothing needed here. */
}
input.raw_input {
  font-family: monospace;
  font-size: inherit;
  color: inherit;
  width: auto;
  /* make sure input baseline aligns with prompt */
  vertical-align: baseline;
  /* padding + margin = 0.5em between prompt and cursor */
  padding: 0em 0.25em;
  margin: 0em 0.25em;
}
input.raw_input:focus {
  box-shadow: none;
}
p.p-space {
  margin-bottom: 10px;
}
div.output_unrecognized {
  padding: 5px;
  font-weight: bold;
  color: red;
}
div.output_unrecognized a {
  color: inherit;
  text-decoration: none;
}
div.output_unrecognized a:hover {
  color: inherit;
  text-decoration: none;
}
.rendered_html {
  color: #000;
  /* any extras will just be numbers: */
}
.rendered_html em {
  font-style: italic;
}
.rendered_html strong {
  font-weight: bold;
}
.rendered_html u {
  text-decoration: underline;
}
.rendered_html :link {
  text-decoration: underline;
}
.rendered_html :visited {
  text-decoration: underline;
}
.rendered_html h1 {
  font-size: 185.7%;
  margin: 1.08em 0 0 0;
  font-weight: bold;
  line-height: 1.0;
}
.rendered_html h2 {
  font-size: 157.1%;
  margin: 1.27em 0 0 0;
  font-weight: bold;
  line-height: 1.0;
}
.rendered_html h3 {
  font-size: 128.6%;
  margin: 1.55em 0 0 0;
  font-weight: bold;
  line-height: 1.0;
}
.rendered_html h4 {
  font-size: 100%;
  margin: 2em 0 0 0;
  font-weight: bold;
  line-height: 1.0;
}
.rendered_html h5 {
  font-size: 100%;
  margin: 2em 0 0 0;
  font-weight: bold;
  line-height: 1.0;
  font-style: italic;
}
.rendered_html h6 {
  font-size: 100%;
  margin: 2em 0 0 0;
  font-weight: bold;
  line-height: 1.0;
  font-style: italic;
}
.rendered_html h1:first-child {
  margin-top: 0.538em;
}
.rendered_html h2:first-child {
  margin-top: 0.636em;
}
.rendered_html h3:first-child {
  margin-top: 0.777em;
}
.rendered_html h4:first-child {
  margin-top: 1em;
}
.rendered_html h5:first-child {
  margin-top: 1em;
}
.rendered_html h6:first-child {
  margin-top: 1em;
}
.rendered_html ul:not(.list-inline),
.rendered_html ol:not(.list-inline) {
  padding-left: 2em;
}
.rendered_html ul {
  list-style: disc;
}
.rendered_html ul ul {
  list-style: square;
  margin-top: 0;
}
.rendered_html ul ul ul {
  list-style: circle;
}
.rendered_html ol {
  list-style: decimal;
}
.rendered_html ol ol {
  list-style: upper-alpha;
  margin-top: 0;
}
.rendered_html ol ol ol {
  list-style: lower-alpha;
}
.rendered_html ol ol ol ol {
  list-style: lower-roman;
}
.rendered_html ol ol ol ol ol {
  list-style: decimal;
}
.rendered_html * + ul {
  margin-top: 1em;
}
.rendered_html * + ol {
  margin-top: 1em;
}
.rendered_html hr {
  color: black;
  background-color: black;
}
.rendered_html pre {
  margin: 1em 2em;
  padding: 0px;
  background-color: #fff;
}
.rendered_html code {
  background-color: #eff0f1;
}
.rendered_html p code {
  padding: 1px 5px;
}
.rendered_html pre code {
  background-color: #fff;
}
.rendered_html pre,
.rendered_html code {
  border: 0;
  color: #000;
  font-size: 100%;
}
.rendered_html blockquote {
  margin: 1em 2em;
}
.rendered_html table {
  margin-left: auto;
  margin-right: auto;
  border: none;
  border-collapse: collapse;
  border-spacing: 0;
  color: black;
  font-size: 12px;
  table-layout: fixed;
}
.rendered_html thead {
  border-bottom: 1px solid black;
  vertical-align: bottom;
}
.rendered_html tr,
.rendered_html th,
.rendered_html td {
  text-align: right;
  vertical-align: middle;
  padding: 0.5em 0.5em;
  line-height: normal;
  white-space: normal;
  max-width: none;
  border: none;
}
.rendered_html th {
  font-weight: bold;
}
.rendered_html tbody tr:nth-child(odd) {
  background: #f5f5f5;
}
.rendered_html tbody tr:hover {
  background: rgba(66, 165, 245, 0.2);
}
.rendered_html * + table {
  margin-top: 1em;
}
.rendered_html p {
  text-align: left;
}
.rendered_html * + p {
  margin-top: 1em;
}
.rendered_html img {
  display: block;
  margin-left: auto;
  margin-right: auto;
}
.rendered_html * + img {
  margin-top: 1em;
}
.rendered_html img,
.rendered_html svg {
  max-width: 100%;
  height: auto;
}
.rendered_html img.unconfined,
.rendered_html svg.unconfined {
  max-width: none;
}
.rendered_html .alert {
  margin-bottom: initial;
}
.rendered_html * + .alert {
  margin-top: 1em;
}
[dir="rtl"] .rendered_html p {
  text-align: right;
}
div.text_cell {
  /* Old browsers */
  display: -webkit-box;
  -webkit-box-orient: horizontal;
  -webkit-box-align: stretch;
  display: -moz-box;
  -moz-box-orient: horizontal;
  -moz-box-align: stretch;
  display: box;
  box-orient: horizontal;
  box-align: stretch;
  /* Modern browsers */
  display: flex;
  flex-direction: row;
  align-items: stretch;
}
@media (max-width: 540px) {
  div.text_cell > div.prompt {
    display: none;
  }
}
div.text_cell_render {
  /*font-family: "Helvetica Neue", Arial, Helvetica, Geneva, sans-serif;*/
  outline: none;
  resize: none;
  width: inherit;
  border-style: none;
  padding: 0.5em 0.5em 0.5em 0.4em;
  color: #000;
  box-sizing: border-box;
  -moz-box-sizing: border-box;
  -webkit-box-sizing: border-box;
}
a.anchor-link:link {
  text-decoration: none;
  padding: 0px 20px;
  visibility: hidden;
}
h1:hover .anchor-link,
h2:hover .anchor-link,
h3:hover .anchor-link,
h4:hover .anchor-link,
h5:hover .anchor-link,
h6:hover .anchor-link {
  visibility: visible;
}
.text_cell.rendered .input_area {
  display: none;
}
.text_cell.rendered .rendered_html {
  overflow-x: auto;
  overflow-y: hidden;
}
.text_cell.rendered .rendered_html tr,
.text_cell.rendered .rendered_html th,
.text_cell.rendered .rendered_html td {
  max-width: none;
}
.text_cell.unrendered .text_cell_render {
  display: none;
}
.text_cell .dropzone .input_area {
  border: 2px dashed #bababa;
  margin: -1px;
}
.cm-header-1,
.cm-header-2,
.cm-header-3,
.cm-header-4,
.cm-header-5,
.cm-header-6 {
  font-weight: bold;
  font-family: "Helvetica Neue", Helvetica, Arial, sans-serif;
}
.cm-header-1 {
  font-size: 185.7%;
}
.cm-header-2 {
  font-size: 157.1%;
}
.cm-header-3 {
  font-size: 128.6%;
}
.cm-header-4 {
  font-size: 110%;
}
.cm-header-5 {
  font-size: 100%;
  font-style: italic;
}
.cm-header-6 {
  font-size: 100%;
  font-style: italic;
}
/*!
*
* IPython notebook webapp
*
*/
@media (max-width: 767px) {
  .notebook_app {
    padding-left: 0px;
    padding-right: 0px;
  }
}
#ipython-main-app {
  box-sizing: border-box;
  -moz-box-sizing: border-box;
  -webkit-box-sizing: border-box;
  height: 100%;
}
div#notebook_panel {
  margin: 0px;
  padding: 0px;
  box-sizing: border-box;
  -moz-box-sizing: border-box;
  -webkit-box-sizing: border-box;
  height: 100%;
}
div#notebook {
  font-size: 14px;
  line-height: 20px;
  overflow-y: hidden;
  overflow-x: auto;
  width: 100%;
  /* This spaces the page away from the edge of the notebook area */
  padding-top: 20px;
  margin: 0px;
  outline: none;
  box-sizing: border-box;
  -moz-box-sizing: border-box;
  -webkit-box-sizing: border-box;
  min-height: 100%;
}
@media not print {
  #notebook-container {
    padding: 15px;
    background-color: #fff;
    min-height: 0;
    -webkit-box-shadow: 0px 0px 12px 1px rgba(87, 87, 87, 0.2);
    box-shadow: 0px 0px 12px 1px rgba(87, 87, 87, 0.2);
  }
}
@media print {
  #notebook-container {
    width: 100%;
  }
}
div.ui-widget-content {
  border: 1px solid #ababab;
  outline: none;
}
pre.dialog {
  background-color: #f7f7f7;
  border: 1px solid #ddd;
  border-radius: 2px;
  padding: 0.4em;
  padding-left: 2em;
}
p.dialog {
  padding: 0.2em;
}
/* Word-wrap output correctly.  This is the CSS3 spelling, though Firefox seems
   to not honor it correctly.  Webkit browsers (Chrome, rekonq, Safari) do.
 */
pre,
code,
kbd,
samp {
  white-space: pre-wrap;
}
#fonttest {
  font-family: monospace;
}
p {
  margin-bottom: 0;
}
.end_space {
  min-height: 100px;
  transition: height .2s ease;
}
.notebook_app > #header {
  -webkit-box-shadow: 0px 0px 12px 1px rgba(87, 87, 87, 0.2);
  box-shadow: 0px 0px 12px 1px rgba(87, 87, 87, 0.2);
}
@media not print {
  .notebook_app {
    background-color: #EEE;
  }
}
kbd {
  border-style: solid;
  border-width: 1px;
  box-shadow: none;
  margin: 2px;
  padding-left: 2px;
  padding-right: 2px;
  padding-top: 1px;
  padding-bottom: 1px;
}
.jupyter-keybindings {
  padding: 1px;
  line-height: 24px;
  border-bottom: 1px solid gray;
}
.jupyter-keybindings input {
  margin: 0;
  padding: 0;
  border: none;
}
.jupyter-keybindings i {
  padding: 6px;
}
.well code {
  background-color: #ffffff;
  border-color: #ababab;
  border-width: 1px;
  border-style: solid;
  padding: 2px;
  padding-top: 1px;
  padding-bottom: 1px;
}
/* CSS for the cell toolbar */
.celltoolbar {
  border: thin solid #CFCFCF;
  border-bottom: none;
  background: #EEE;
  border-radius: 2px 2px 0px 0px;
  width: 100%;
  height: 29px;
  padding-right: 4px;
  /* Old browsers */
  display: -webkit-box;
  -webkit-box-orient: horizontal;
  -webkit-box-align: stretch;
  display: -moz-box;
  -moz-box-orient: horizontal;
  -moz-box-align: stretch;
  display: box;
  box-orient: horizontal;
  box-align: stretch;
  /* Modern browsers */
  display: flex;
  flex-direction: row;
  align-items: stretch;
  /* Old browsers */
  -webkit-box-pack: end;
  -moz-box-pack: end;
  box-pack: end;
  /* Modern browsers */
  justify-content: flex-end;
  display: -webkit-flex;
}
@media print {
  .celltoolbar {
    display: none;
  }
}
.ctb_hideshow {
  display: none;
  vertical-align: bottom;
}
/* ctb_show is added to the ctb_hideshow div to show the cell toolbar.
   Cell toolbars are only shown when the ctb_global_show class is also set.
*/
.ctb_global_show .ctb_show.ctb_hideshow {
  display: block;
}
.ctb_global_show .ctb_show + .input_area,
.ctb_global_show .ctb_show + div.text_cell_input,
.ctb_global_show .ctb_show ~ div.text_cell_render {
  border-top-right-radius: 0px;
  border-top-left-radius: 0px;
}
.ctb_global_show .ctb_show ~ div.text_cell_render {
  border: 1px solid #cfcfcf;
}
.celltoolbar {
  font-size: 87%;
  padding-top: 3px;
}
.celltoolbar select {
  display: block;
  width: 100%;
  height: 32px;
  padding: 6px 12px;
  font-size: 13px;
  line-height: 1.42857143;
  color: #555555;
  background-color: #fff;
  background-image: none;
  border: 1px solid #ccc;
  border-radius: 2px;
  -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075);
  box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075);
  -webkit-transition: border-color ease-in-out .15s, box-shadow ease-in-out .15s;
  -o-transition: border-color ease-in-out .15s, box-shadow ease-in-out .15s;
  transition: border-color ease-in-out .15s, box-shadow ease-in-out .15s;
  height: 30px;
  padding: 5px 10px;
  font-size: 12px;
  line-height: 1.5;
  border-radius: 1px;
  width: inherit;
  font-size: inherit;
  height: 22px;
  padding: 0px;
  display: inline-block;
}
.celltoolbar select:focus {
  border-color: #66afe9;
  outline: 0;
  -webkit-box-shadow: inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6);
  box-shadow: inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6);
}
.celltoolbar select::-moz-placeholder {
  color: #999;
  opacity: 1;
}
.celltoolbar select:-ms-input-placeholder {
  color: #999;
}
.celltoolbar select::-webkit-input-placeholder {
  color: #999;
}
.celltoolbar select::-ms-expand {
  border: 0;
  background-color: transparent;
}
.celltoolbar select[disabled],
.celltoolbar select[readonly],
fieldset[disabled] .celltoolbar select {
  background-color: #eeeeee;
  opacity: 1;
}
.celltoolbar select[disabled],
fieldset[disabled] .celltoolbar select {
  cursor: not-allowed;
}
textarea.celltoolbar select {
  height: auto;
}
select.celltoolbar select {
  height: 30px;
  line-height: 30px;
}
textarea.celltoolbar select,
select[multiple].celltoolbar select {
  height: auto;
}
.celltoolbar label {
  margin-left: 5px;
  margin-right: 5px;
}
.tags_button_container {
  width: 100%;
  display: flex;
}
.tag-container {
  display: flex;
  flex-direction: row;
  flex-grow: 1;
  overflow: hidden;
  position: relative;
}
.tag-container > * {
  margin: 0 4px;
}
.remove-tag-btn {
  margin-left: 4px;
}
.tags-input {
  display: flex;
}
.cell-tag:last-child:after {
  content: "";
  position: absolute;
  right: 0;
  width: 40px;
  height: 100%;
  /* Fade to background color of cell toolbar */
  background: linear-gradient(to right, rgba(0, 0, 0, 0), #EEE);
}
.tags-input > * {
  margin-left: 4px;
}
.cell-tag,
.tags-input input,
.tags-input button {
  display: block;
  width: 100%;
  height: 32px;
  padding: 6px 12px;
  font-size: 13px;
  line-height: 1.42857143;
  color: #555555;
  background-color: #fff;
  background-image: none;
  border: 1px solid #ccc;
  border-radius: 2px;
  -webkit-box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075);
  box-shadow: inset 0 1px 1px rgba(0, 0, 0, 0.075);
  -webkit-transition: border-color ease-in-out .15s, box-shadow ease-in-out .15s;
  -o-transition: border-color ease-in-out .15s, box-shadow ease-in-out .15s;
  transition: border-color ease-in-out .15s, box-shadow ease-in-out .15s;
  height: 30px;
  padding: 5px 10px;
  font-size: 12px;
  line-height: 1.5;
  border-radius: 1px;
  box-shadow: none;
  width: inherit;
  font-size: inherit;
  height: 22px;
  line-height: 22px;
  padding: 0px 4px;
  display: inline-block;
}
.cell-tag:focus,
.tags-input input:focus,
.tags-input button:focus {
  border-color: #66afe9;
  outline: 0;
  -webkit-box-shadow: inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6);
  box-shadow: inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6);
}
.cell-tag::-moz-placeholder,
.tags-input input::-moz-placeholder,
.tags-input button::-moz-placeholder {
  color: #999;
  opacity: 1;
}
.cell-tag:-ms-input-placeholder,
.tags-input input:-ms-input-placeholder,
.tags-input button:-ms-input-placeholder {
  color: #999;
}
.cell-tag::-webkit-input-placeholder,
.tags-input input::-webkit-input-placeholder,
.tags-input button::-webkit-input-placeholder {
  color: #999;
}
.cell-tag::-ms-expand,
.tags-input input::-ms-expand,
.tags-input button::-ms-expand {
  border: 0;
  background-color: transparent;
}
.cell-tag[disabled],
.tags-input input[disabled],
.tags-input button[disabled],
.cell-tag[readonly],
.tags-input input[readonly],
.tags-input button[readonly],
fieldset[disabled] .cell-tag,
fieldset[disabled] .tags-input input,
fieldset[disabled] .tags-input button {
  background-color: #eeeeee;
  opacity: 1;
}
.cell-tag[disabled],
.tags-input input[disabled],
.tags-input button[disabled],
fieldset[disabled] .cell-tag,
fieldset[disabled] .tags-input input,
fieldset[disabled] .tags-input button {
  cursor: not-allowed;
}
textarea.cell-tag,
textarea.tags-input input,
textarea.tags-input button {
  height: auto;
}
select.cell-tag,
select.tags-input input,
select.tags-input button {
  height: 30px;
  line-height: 30px;
}
textarea.cell-tag,
textarea.tags-input input,
textarea.tags-input button,
select[multiple].cell-tag,
select[multiple].tags-input input,
select[multiple].tags-input button {
  height: auto;
}
.cell-tag,
.tags-input button {
  padding: 0px 4px;
}
.cell-tag {
  background-color: #fff;
  white-space: nowrap;
}
.tags-input input[type=text]:focus {
  outline: none;
  box-shadow: none;
  border-color: #ccc;
}
.completions {
  position: absolute;
  z-index: 110;
  overflow: hidden;
  border: 1px solid #ababab;
  border-radius: 2px;
  -webkit-box-shadow: 0px 6px 10px -1px #adadad;
  box-shadow: 0px 6px 10px -1px #adadad;
  line-height: 1;
}
.completions select {
  background: white;
  outline: none;
  border: none;
  padding: 0px;
  margin: 0px;
  overflow: auto;
  font-family: monospace;
  font-size: 110%;
  color: #000;
  width: auto;
}
.completions select option.context {
  color: #286090;
}
#kernel_logo_widget .current_kernel_logo {
  display: none;
  margin-top: -1px;
  margin-bottom: -1px;
  width: 32px;
  height: 32px;
}
[dir="rtl"] #kernel_logo_widget {
  float: left !important;
  float: left;
}
.modal .modal-body .move-path {
  display: flex;
  flex-direction: row;
  justify-content: space;
  align-items: center;
}
.modal .modal-body .move-path .server-root {
  padding-right: 20px;
}
.modal .modal-body .move-path .path-input {
  flex: 1;
}
#menubar {
  box-sizing: border-box;
  -moz-box-sizing: border-box;
  -webkit-box-sizing: border-box;
  margin-top: 1px;
}
#menubar .navbar {
  border-top: 1px;
  border-radius: 0px 0px 2px 2px;
  margin-bottom: 0px;
}
#menubar .navbar-toggle {
  float: left;
  padding-top: 7px;
  padding-bottom: 7px;
  border: none;
}
#menubar .navbar-collapse {
  clear: left;
}
[dir="rtl"] #menubar .navbar-toggle {
  float: right;
}
[dir="rtl"] #menubar .navbar-collapse {
  clear: right;
}
[dir="rtl"] #menubar .navbar-nav {
  float: right;
}
[dir="rtl"] #menubar .nav {
  padding-right: 0px;
}
[dir="rtl"] #menubar .navbar-nav > li {
  float: right;
}
[dir="rtl"] #menubar .navbar-right {
  float: left !important;
}
[dir="rtl"] ul.dropdown-menu {
  text-align: right;
  left: auto;
}
[dir="rtl"] ul#new-menu.dropdown-menu {
  right: auto;
  left: 0;
}
.nav-wrapper {
  border-bottom: 1px solid #e7e7e7;
}
i.menu-icon {
  padding-top: 4px;
}
[dir="rtl"] i.menu-icon.pull-right {
  float: left !important;
  float: left;
}
ul#help_menu li a {
  overflow: hidden;
  padding-right: 2.2em;
}
ul#help_menu li a i {
  margin-right: -1.2em;
}
[dir="rtl"] ul#help_menu li a {
  padding-left: 2.2em;
}
[dir="rtl"] ul#help_menu li a i {
  margin-right: 0;
  margin-left: -1.2em;
}
[dir="rtl"] ul#help_menu li a i.pull-right {
  float: left !important;
  float: left;
}
.dropdown-submenu {
  position: relative;
}
.dropdown-submenu > .dropdown-menu {
  top: 0;
  left: 100%;
  margin-top: -6px;
  margin-left: -1px;
}
[dir="rtl"] .dropdown-submenu > .dropdown-menu {
  right: 100%;
  margin-right: -1px;
}
.dropdown-submenu:hover > .dropdown-menu {
  display: block;
}
.dropdown-submenu > a:after {
  display: inline-block;
  font: normal normal normal 14px/1 FontAwesome;
  font-size: inherit;
  text-rendering: auto;
  -webkit-font-smoothing: antialiased;
  -moz-osx-font-smoothing: grayscale;
  display: block;
  content: "\f0da";
  float: right;
  color: #333333;
  margin-top: 2px;
  margin-right: -10px;
}
.dropdown-submenu > a:after.fa-pull-left {
  margin-right: .3em;
}
.dropdown-submenu > a:after.fa-pull-right {
  margin-left: .3em;
}
.dropdown-submenu > a:after.pull-left {
  margin-right: .3em;
}
.dropdown-submenu > a:after.pull-right {
  margin-left: .3em;
}
[dir="rtl"] .dropdown-submenu > a:after {
  float: left;
  content: "\f0d9";
  margin-right: 0;
  margin-left: -10px;
}
.dropdown-submenu:hover > a:after {
  color: #262626;
}
.dropdown-submenu.pull-left {
  float: none;
}
.dropdown-submenu.pull-left > .dropdown-menu {
  left: -100%;
  margin-left: 10px;
}
#notification_area {
  float: right !important;
  float: right;
  z-index: 10;
}
[dir="rtl"] #notification_area {
  float: left !important;
  float: left;
}
.indicator_area {
  float: right !important;
  float: right;
  color: #777;
  margin-left: 5px;
  margin-right: 5px;
  width: 11px;
  z-index: 10;
  text-align: center;
  width: auto;
}
[dir="rtl"] .indicator_area {
  float: left !important;
  float: left;
}
#kernel_indicator {
  float: right !important;
  float: right;
  color: #777;
  margin-left: 5px;
  margin-right: 5px;
  width: 11px;
  z-index: 10;
  text-align: center;
  width: auto;
  border-left: 1px solid;
}
#kernel_indicator .kernel_indicator_name {
  padding-left: 5px;
  padding-right: 5px;
}
[dir="rtl"] #kernel_indicator {
  float: left !important;
  float: left;
  border-left: 0;
  border-right: 1px solid;
}
#modal_indicator {
  float: right !important;
  float: right;
  color: #777;
  margin-left: 5px;
  margin-right: 5px;
  width: 11px;
  z-index: 10;
  text-align: center;
  width: auto;
}
[dir="rtl"] #modal_indicator {
  float: left !important;
  float: left;
}
#readonly-indicator {
  float: right !important;
  float: right;
  color: #777;
  margin-left: 5px;
  margin-right: 5px;
  width: 11px;
  z-index: 10;
  text-align: center;
  width: auto;
  margin-top: 2px;
  margin-bottom: 0px;
  margin-left: 0px;
  margin-right: 0px;
  display: none;
}
.modal_indicator:before {
  width: 1.28571429em;
  text-align: center;
}
.edit_mode .modal_indicator:before {
  display: inline-block;
  font: normal normal normal 14px/1 FontAwesome;
  font-size: inherit;
  text-rendering: auto;
  -webkit-font-smoothing: antialiased;
  -moz-osx-font-smoothing: grayscale;
  content: "\f040";
}
.edit_mode .modal_indicator:before.fa-pull-left {
  margin-right: .3em;
}
.edit_mode .modal_indicator:before.fa-pull-right {
  margin-left: .3em;
}
.edit_mode .modal_indicator:before.pull-left {
  margin-right: .3em;
}
.edit_mode .modal_indicator:before.pull-right {
  margin-left: .3em;
}
.command_mode .modal_indicator:before {
  display: inline-block;
  font: normal normal normal 14px/1 FontAwesome;
  font-size: inherit;
  text-rendering: auto;
  -webkit-font-smoothing: antialiased;
  -moz-osx-font-smoothing: grayscale;
  content: ' ';
}
.command_mode .modal_indicator:before.fa-pull-left {
  margin-right: .3em;
}
.command_mode .modal_indicator:before.fa-pull-right {
  margin-left: .3em;
}
.command_mode .modal_indicator:before.pull-left {
  margin-right: .3em;
}
.command_mode .modal_indicator:before.pull-right {
  margin-left: .3em;
}
.kernel_idle_icon:before {
  display: inline-block;
  font: normal normal normal 14px/1 FontAwesome;
  font-size: inherit;
  text-rendering: auto;
  -webkit-font-smoothing: antialiased;
  -moz-osx-font-smoothing: grayscale;
  content: "\f10c";
}
.kernel_idle_icon:before.fa-pull-left {
  margin-right: .3em;
}
.kernel_idle_icon:before.fa-pull-right {
  margin-left: .3em;
}
.kernel_idle_icon:before.pull-left {
  margin-right: .3em;
}
.kernel_idle_icon:before.pull-right {
  margin-left: .3em;
}
.kernel_busy_icon:before {
  display: inline-block;
  font: normal normal normal 14px/1 FontAwesome;
  font-size: inherit;
  text-rendering: auto;
  -webkit-font-smoothing: antialiased;
  -moz-osx-font-smoothing: grayscale;
  content: "\f111";
}
.kernel_busy_icon:before.fa-pull-left {
  margin-right: .3em;
}
.kernel_busy_icon:before.fa-pull-right {
  margin-left: .3em;
}
.kernel_busy_icon:before.pull-left {
  margin-right: .3em;
}
.kernel_busy_icon:before.pull-right {
  margin-left: .3em;
}
.kernel_dead_icon:before {
  display: inline-block;
  font: normal normal normal 14px/1 FontAwesome;
  font-size: inherit;
  text-rendering: auto;
  -webkit-font-smoothing: antialiased;
  -moz-osx-font-smoothing: grayscale;
  content: "\f1e2";
}
.kernel_dead_icon:before.fa-pull-left {
  margin-right: .3em;
}
.kernel_dead_icon:before.fa-pull-right {
  margin-left: .3em;
}
.kernel_dead_icon:before.pull-left {
  margin-right: .3em;
}
.kernel_dead_icon:before.pull-right {
  margin-left: .3em;
}
.kernel_disconnected_icon:before {
  display: inline-block;
  font: normal normal normal 14px/1 FontAwesome;
  font-size: inherit;
  text-rendering: auto;
  -webkit-font-smoothing: antialiased;
  -moz-osx-font-smoothing: grayscale;
  content: "\f127";
}
.kernel_disconnected_icon:before.fa-pull-left {
  margin-right: .3em;
}
.kernel_disconnected_icon:before.fa-pull-right {
  margin-left: .3em;
}
.kernel_disconnected_icon:before.pull-left {
  margin-right: .3em;
}
.kernel_disconnected_icon:before.pull-right {
  margin-left: .3em;
}
.notification_widget {
  color: #777;
  z-index: 10;
  background: rgba(240, 240, 240, 0.5);
  margin-right: 4px;
  color: #333;
  background-color: #fff;
  border-color: #ccc;
}
.notification_widget:focus,
.notification_widget.focus {
  color: #333;
  background-color: #e6e6e6;
  border-color: #8c8c8c;
}
.notification_widget:hover {
  color: #333;
  background-color: #e6e6e6;
  border-color: #adadad;
}
.notification_widget:active,
.notification_widget.active,
.open > .dropdown-toggle.notification_widget {
  color: #333;
  background-color: #e6e6e6;
  border-color: #adadad;
}
.notification_widget:active:hover,
.notification_widget.active:hover,
.open > .dropdown-toggle.notification_widget:hover,
.notification_widget:active:focus,
.notification_widget.active:focus,
.open > .dropdown-toggle.notification_widget:focus,
.notification_widget:active.focus,
.notification_widget.active.focus,
.open > .dropdown-toggle.notification_widget.focus {
  color: #333;
  background-color: #d4d4d4;
  border-color: #8c8c8c;
}
.notification_widget:active,
.notification_widget.active,
.open > .dropdown-toggle.notification_widget {
  background-image: none;
}
.notification_widget.disabled:hover,
.notification_widget[disabled]:hover,
fieldset[disabled] .notification_widget:hover,
.notification_widget.disabled:focus,
.notification_widget[disabled]:focus,
fieldset[disabled] .notification_widget:focus,
.notification_widget.disabled.focus,
.notification_widget[disabled].focus,
fieldset[disabled] .notification_widget.focus {
  background-color: #fff;
  border-color: #ccc;
}
.notification_widget .badge {
  color: #fff;
  background-color: #333;
}
.notification_widget.warning {
  color: #fff;
  background-color: #f0ad4e;
  border-color: #eea236;
}
.notification_widget.warning:focus,
.notification_widget.warning.focus {
  color: #fff;
  background-color: #ec971f;
  border-color: #985f0d;
}
.notification_widget.warning:hover {
  color: #fff;
  background-color: #ec971f;
  border-color: #d58512;
}
.notification_widget.warning:active,
.notification_widget.warning.active,
.open > .dropdown-toggle.notification_widget.warning {
  color: #fff;
  background-color: #ec971f;
  border-color: #d58512;
}
.notification_widget.warning:active:hover,
.notification_widget.warning.active:hover,
.open > .dropdown-toggle.notification_widget.warning:hover,
.notification_widget.warning:active:focus,
.notification_widget.warning.active:focus,
.open > .dropdown-toggle.notification_widget.warning:focus,
.notification_widget.warning:active.focus,
.notification_widget.warning.active.focus,
.open > .dropdown-toggle.notification_widget.warning.focus {
  color: #fff;
  background-color: #d58512;
  border-color: #985f0d;
}
.notification_widget.warning:active,
.notification_widget.warning.active,
.open > .dropdown-toggle.notification_widget.warning {
  background-image: none;
}
.notification_widget.warning.disabled:hover,
.notification_widget.warning[disabled]:hover,
fieldset[disabled] .notification_widget.warning:hover,
.notification_widget.warning.disabled:focus,
.notification_widget.warning[disabled]:focus,
fieldset[disabled] .notification_widget.warning:focus,
.notification_widget.warning.disabled.focus,
.notification_widget.warning[disabled].focus,
fieldset[disabled] .notification_widget.warning.focus {
  background-color: #f0ad4e;
  border-color: #eea236;
}
.notification_widget.warning .badge {
  color: #f0ad4e;
  background-color: #fff;
}
.notification_widget.success {
  color: #fff;
  background-color: #5cb85c;
  border-color: #4cae4c;
}
.notification_widget.success:focus,
.notification_widget.success.focus {
  color: #fff;
  background-color: #449d44;
  border-color: #255625;
}
.notification_widget.success:hover {
  color: #fff;
  background-color: #449d44;
  border-color: #398439;
}
.notification_widget.success:active,
.notification_widget.success.active,
.open > .dropdown-toggle.notification_widget.success {
  color: #fff;
  background-color: #449d44;
  border-color: #398439;
}
.notification_widget.success:active:hover,
.notification_widget.success.active:hover,
.open > .dropdown-toggle.notification_widget.success:hover,
.notification_widget.success:active:focus,
.notification_widget.success.active:focus,
.open > .dropdown-toggle.notification_widget.success:focus,
.notification_widget.success:active.focus,
.notification_widget.success.active.focus,
.open > .dropdown-toggle.notification_widget.success.focus {
  color: #fff;
  background-color: #398439;
  border-color: #255625;
}
.notification_widget.success:active,
.notification_widget.success.active,
.open > .dropdown-toggle.notification_widget.success {
  background-image: none;
}
.notification_widget.success.disabled:hover,
.notification_widget.success[disabled]:hover,
fieldset[disabled] .notification_widget.success:hover,
.notification_widget.success.disabled:focus,
.notification_widget.success[disabled]:focus,
fieldset[disabled] .notification_widget.success:focus,
.notification_widget.success.disabled.focus,
.notification_widget.success[disabled].focus,
fieldset[disabled] .notification_widget.success.focus {
  background-color: #5cb85c;
  border-color: #4cae4c;
}
.notification_widget.success .badge {
  color: #5cb85c;
  background-color: #fff;
}
.notification_widget.info {
  color: #fff;
  background-color: #5bc0de;
  border-color: #46b8da;
}
.notification_widget.info:focus,
.notification_widget.info.focus {
  color: #fff;
  background-color: #31b0d5;
  border-color: #1b6d85;
}
.notification_widget.info:hover {
  color: #fff;
  background-color: #31b0d5;
  border-color: #269abc;
}
.notification_widget.info:active,
.notification_widget.info.active,
.open > .dropdown-toggle.notification_widget.info {
  color: #fff;
  background-color: #31b0d5;
  border-color: #269abc;
}
.notification_widget.info:active:hover,
.notification_widget.info.active:hover,
.open > .dropdown-toggle.notification_widget.info:hover,
.notification_widget.info:active:focus,
.notification_widget.info.active:focus,
.open > .dropdown-toggle.notification_widget.info:focus,
.notification_widget.info:active.focus,
.notification_widget.info.active.focus,
.open > .dropdown-toggle.notification_widget.info.focus {
  color: #fff;
  background-color: #269abc;
  border-color: #1b6d85;
}
.notification_widget.info:active,
.notification_widget.info.active,
.open > .dropdown-toggle.notification_widget.info {
  background-image: none;
}
.notification_widget.info.disabled:hover,
.notification_widget.info[disabled]:hover,
fieldset[disabled] .notification_widget.info:hover,
.notification_widget.info.disabled:focus,
.notification_widget.info[disabled]:focus,
fieldset[disabled] .notification_widget.info:focus,
.notification_widget.info.disabled.focus,
.notification_widget.info[disabled].focus,
fieldset[disabled] .notification_widget.info.focus {
  background-color: #5bc0de;
  border-color: #46b8da;
}
.notification_widget.info .badge {
  color: #5bc0de;
  background-color: #fff;
}
.notification_widget.danger {
  color: #fff;
  background-color: #d9534f;
  border-color: #d43f3a;
}
.notification_widget.danger:focus,
.notification_widget.danger.focus {
  color: #fff;
  background-color: #c9302c;
  border-color: #761c19;
}
.notification_widget.danger:hover {
  color: #fff;
  background-color: #c9302c;
  border-color: #ac2925;
}
.notification_widget.danger:active,
.notification_widget.danger.active,
.open > .dropdown-toggle.notification_widget.danger {
  color: #fff;
  background-color: #c9302c;
  border-color: #ac2925;
}
.notification_widget.danger:active:hover,
.notification_widget.danger.active:hover,
.open > .dropdown-toggle.notification_widget.danger:hover,
.notification_widget.danger:active:focus,
.notification_widget.danger.active:focus,
.open > .dropdown-toggle.notification_widget.danger:focus,
.notification_widget.danger:active.focus,
.notification_widget.danger.active.focus,
.open > .dropdown-toggle.notification_widget.danger.focus {
  color: #fff;
  background-color: #ac2925;
  border-color: #761c19;
}
.notification_widget.danger:active,
.notification_widget.danger.active,
.open > .dropdown-toggle.notification_widget.danger {
  background-image: none;
}
.notification_widget.danger.disabled:hover,
.notification_widget.danger[disabled]:hover,
fieldset[disabled] .notification_widget.danger:hover,
.notification_widget.danger.disabled:focus,
.notification_widget.danger[disabled]:focus,
fieldset[disabled] .notification_widget.danger:focus,
.notification_widget.danger.disabled.focus,
.notification_widget.danger[disabled].focus,
fieldset[disabled] .notification_widget.danger.focus {
  background-color: #d9534f;
  border-color: #d43f3a;
}
.notification_widget.danger .badge {
  color: #d9534f;
  background-color: #fff;
}
div#pager {
  background-color: #fff;
  font-size: 14px;
  line-height: 20px;
  overflow: hidden;
  display: none;
  position: fixed;
  bottom: 0px;
  width: 100%;
  max-height: 50%;
  padding-top: 8px;
  -webkit-box-shadow: 0px 0px 12px 1px rgba(87, 87, 87, 0.2);
  box-shadow: 0px 0px 12px 1px rgba(87, 87, 87, 0.2);
  /* Display over codemirror */
  z-index: 100;
  /* Hack which prevents jquery ui resizable from changing top. */
  top: auto !important;
}
div#pager pre {
  line-height: 1.21429em;
  color: #000;
  background-color: #f7f7f7;
  padding: 0.4em;
}
div#pager #pager-button-area {
  position: absolute;
  top: 8px;
  right: 20px;
}
div#pager #pager-contents {
  position: relative;
  overflow: auto;
  width: 100%;
  height: 100%;
}
div#pager #pager-contents #pager-container {
  position: relative;
  padding: 15px 0px;
  box-sizing: border-box;
  -moz-box-sizing: border-box;
  -webkit-box-sizing: border-box;
}
div#pager .ui-resizable-handle {
  top: 0px;
  height: 8px;
  background: #f7f7f7;
  border-top: 1px solid #cfcfcf;
  border-bottom: 1px solid #cfcfcf;
  /* This injects handle bars (a short, wide = symbol) for 
        the resize handle. */
}
div#pager .ui-resizable-handle::after {
  content: '';
  top: 2px;
  left: 50%;
  height: 3px;
  width: 30px;
  margin-left: -15px;
  position: absolute;
  border-top: 1px solid #cfcfcf;
}
.quickhelp {
  /* Old browsers */
  display: -webkit-box;
  -webkit-box-orient: horizontal;
  -webkit-box-align: stretch;
  display: -moz-box;
  -moz-box-orient: horizontal;
  -moz-box-align: stretch;
  display: box;
  box-orient: horizontal;
  box-align: stretch;
  /* Modern browsers */
  display: flex;
  flex-direction: row;
  align-items: stretch;
  line-height: 1.8em;
}
.shortcut_key {
  display: inline-block;
  width: 21ex;
  text-align: right;
  font-family: monospace;
}
.shortcut_descr {
  display: inline-block;
  /* Old browsers */
  -webkit-box-flex: 1;
  -moz-box-flex: 1;
  box-flex: 1;
  /* Modern browsers */
  flex: 1;
}
span.save_widget {
  height: 30px;
  margin-top: 4px;
  display: flex;
  justify-content: flex-start;
  align-items: baseline;
  width: 50%;
  flex: 1;
}
span.save_widget span.filename {
  height: 100%;
  line-height: 1em;
  margin-left: 16px;
  border: none;
  font-size: 146.5%;
  text-overflow: ellipsis;
  overflow: hidden;
  white-space: nowrap;
  border-radius: 2px;
}
span.save_widget span.filename:hover {
  background-color: #e6e6e6;
}
[dir="rtl"] span.save_widget.pull-left {
  float: right !important;
  float: right;
}
[dir="rtl"] span.save_widget span.filename {
  margin-left: 0;
  margin-right: 16px;
}
span.checkpoint_status,
span.autosave_status {
  font-size: small;
  white-space: nowrap;
  padding: 0 5px;
}
@media (max-width: 767px) {
  span.save_widget {
    font-size: small;
    padding: 0 0 0 5px;
  }
  span.checkpoint_status,
  span.autosave_status {
    display: none;
  }
}
@media (min-width: 768px) and (max-width: 991px) {
  span.checkpoint_status {
    display: none;
  }
  span.autosave_status {
    font-size: x-small;
  }
}
.toolbar {
  padding: 0px;
  margin-left: -5px;
  margin-top: 2px;
  margin-bottom: 5px;
  box-sizing: border-box;
  -moz-box-sizing: border-box;
  -webkit-box-sizing: border-box;
}
.toolbar select,
.toolbar label {
  width: auto;
  vertical-align: middle;
  margin-right: 2px;
  margin-bottom: 0px;
  display: inline;
  font-size: 92%;
  margin-left: 0.3em;
  margin-right: 0.3em;
  padding: 0px;
  padding-top: 3px;
}
.toolbar .btn {
  padding: 2px 8px;
}
.toolbar .btn-group {
  margin-top: 0px;
  margin-left: 5px;
}
.toolbar-btn-label {
  margin-left: 6px;
}
#maintoolbar {
  margin-bottom: -3px;
  margin-top: -8px;
  border: 0px;
  min-height: 27px;
  margin-left: 0px;
  padding-top: 11px;
  padding-bottom: 3px;
}
#maintoolbar .navbar-text {
  float: none;
  vertical-align: middle;
  text-align: right;
  margin-left: 5px;
  margin-right: 0px;
  margin-top: 0px;
}
.select-xs {
  height: 24px;
}
[dir="rtl"] .btn-group > .btn,
.btn-group-vertical > .btn {
  float: right;
}
.pulse,
.dropdown-menu > li > a.pulse,
li.pulse > a.dropdown-toggle,
li.pulse.open > a.dropdown-toggle {
  background-color: #F37626;
  color: white;
}
/**
 * Primary styles
 *
 * Author: Jupyter Development Team
 */
/** WARNING IF YOU ARE EDITTING THIS FILE, if this is a .css file, It has a lot
 * of chance of beeing generated from the ../less/[samename].less file, you can
 * try to get back the less file by reverting somme commit in history
 **/
/*
 * We'll try to get something pretty, so we
 * have some strange css to have the scroll bar on
 * the left with fix button on the top right of the tooltip
 */
@-moz-keyframes fadeOut {
  from {
    opacity: 1;
  }
  to {
    opacity: 0;
  }
}
@-webkit-keyframes fadeOut {
  from {
    opacity: 1;
  }
  to {
    opacity: 0;
  }
}
@-moz-keyframes fadeIn {
  from {
    opacity: 0;
  }
  to {
    opacity: 1;
  }
}
@-webkit-keyframes fadeIn {
  from {
    opacity: 0;
  }
  to {
    opacity: 1;
  }
}
/*properties of tooltip after "expand"*/
.bigtooltip {
  overflow: auto;
  height: 200px;
  -webkit-transition-property: height;
  -webkit-transition-duration: 500ms;
  -moz-transition-property: height;
  -moz-transition-duration: 500ms;
  transition-property: height;
  transition-duration: 500ms;
}
/*properties of tooltip before "expand"*/
.smalltooltip {
  -webkit-transition-property: height;
  -webkit-transition-duration: 500ms;
  -moz-transition-property: height;
  -moz-transition-duration: 500ms;
  transition-property: height;
  transition-duration: 500ms;
  text-overflow: ellipsis;
  overflow: hidden;
  height: 80px;
}
.tooltipbuttons {
  position: absolute;
  padding-right: 15px;
  top: 0px;
  right: 0px;
}
.tooltiptext {
  /*avoid the button to overlap on some docstring*/
  padding-right: 30px;
}
.ipython_tooltip {
  max-width: 700px;
  /*fade-in animation when inserted*/
  -webkit-animation: fadeOut 400ms;
  -moz-animation: fadeOut 400ms;
  animation: fadeOut 400ms;
  -webkit-animation: fadeIn 400ms;
  -moz-animation: fadeIn 400ms;
  animation: fadeIn 400ms;
  vertical-align: middle;
  background-color: #f7f7f7;
  overflow: visible;
  border: #ababab 1px solid;
  outline: none;
  padding: 3px;
  margin: 0px;
  padding-left: 7px;
  font-family: monospace;
  min-height: 50px;
  -moz-box-shadow: 0px 6px 10px -1px #adadad;
  -webkit-box-shadow: 0px 6px 10px -1px #adadad;
  box-shadow: 0px 6px 10px -1px #adadad;
  border-radius: 2px;
  position: absolute;
  z-index: 1000;
}
.ipython_tooltip a {
  float: right;
}
.ipython_tooltip .tooltiptext pre {
  border: 0;
  border-radius: 0;
  font-size: 100%;
  background-color: #f7f7f7;
}
.pretooltiparrow {
  left: 0px;
  margin: 0px;
  top: -16px;
  width: 40px;
  height: 16px;
  overflow: hidden;
  position: absolute;
}
.pretooltiparrow:before {
  background-color: #f7f7f7;
  border: 1px #ababab solid;
  z-index: 11;
  content: "";
  position: absolute;
  left: 15px;
  top: 10px;
  width: 25px;
  height: 25px;
  -webkit-transform: rotate(45deg);
  -moz-transform: rotate(45deg);
  -ms-transform: rotate(45deg);
  -o-transform: rotate(45deg);
}
ul.typeahead-list i {
  margin-left: -10px;
  width: 18px;
}
[dir="rtl"] ul.typeahead-list i {
  margin-left: 0;
  margin-right: -10px;
}
ul.typeahead-list {
  max-height: 80vh;
  overflow: auto;
}
ul.typeahead-list > li > a {
  /** Firefox bug **/
  /* see https://github.com/jupyter/notebook/issues/559 */
  white-space: normal;
}
ul.typeahead-list  > li > a.pull-right {
  float: left !important;
  float: left;
}
[dir="rtl"] .typeahead-list {
  text-align: right;
}
.cmd-palette .modal-body {
  padding: 7px;
}
.cmd-palette form {
  background: white;
}
.cmd-palette input {
  outline: none;
}
.no-shortcut {
  min-width: 20px;
  color: transparent;
}
[dir="rtl"] .no-shortcut.pull-right {
  float: left !important;
  float: left;
}
[dir="rtl"] .command-shortcut.pull-right {
  float: left !important;
  float: left;
}
.command-shortcut:before {
  content: "(command mode)";
  padding-right: 3px;
  color: #777777;
}
.edit-shortcut:before {
  content: "(edit)";
  padding-right: 3px;
  color: #777777;
}
[dir="rtl"] .edit-shortcut.pull-right {
  float: left !important;
  float: left;
}
#find-and-replace #replace-preview .match,
#find-and-replace #replace-preview .insert {
  background-color: #BBDEFB;
  border-color: #90CAF9;
  border-style: solid;
  border-width: 1px;
  border-radius: 0px;
}
[dir="ltr"] #find-and-replace .input-group-btn + .form-control {
  border-left: none;
}
[dir="rtl"] #find-and-replace .input-group-btn + .form-control {
  border-right: none;
}
#find-and-replace #replace-preview .replace .match {
  background-color: #FFCDD2;
  border-color: #EF9A9A;
  border-radius: 0px;
}
#find-and-replace #replace-preview .replace .insert {
  background-color: #C8E6C9;
  border-color: #A5D6A7;
  border-radius: 0px;
}
#find-and-replace #replace-preview {
  max-height: 60vh;
  overflow: auto;
}
#find-and-replace #replace-preview pre {
  padding: 5px 10px;
}
.terminal-app {
  background: #EEE;
}
.terminal-app #header {
  background: #fff;
  -webkit-box-shadow: 0px 0px 12px 1px rgba(87, 87, 87, 0.2);
  box-shadow: 0px 0px 12px 1px rgba(87, 87, 87, 0.2);
}
.terminal-app .terminal {
  width: 100%;
  float: left;
  font-family: monospace;
  color: white;
  background: black;
  padding: 0.4em;
  border-radius: 2px;
  -webkit-box-shadow: 0px 0px 12px 1px rgba(87, 87, 87, 0.4);
  box-shadow: 0px 0px 12px 1px rgba(87, 87, 87, 0.4);
}
.terminal-app .terminal,
.terminal-app .terminal dummy-screen {
  line-height: 1em;
  font-size: 14px;
}
.terminal-app .terminal .xterm-rows {
  padding: 10px;
}
.terminal-app .terminal-cursor {
  color: black;
  background: white;
}
.terminal-app #terminado-container {
  margin-top: 20px;
}
/*# sourceMappingURL=style.min.css.map */
    </style>
<style type="text/css">
    .highlight .hll { background-color: #ffffcc }
.highlight  { background: #f8f8f8; }
.highlight .c { color: #408080; font-style: italic } /* Comment */
.highlight .err { border: 1px solid #FF0000 } /* Error */
.highlight .k { color: #008000; font-weight: bold } /* Keyword */
.highlight .o { color: #666666 } /* Operator */
.highlight .ch { color: #408080; font-style: italic } /* Comment.Hashbang */
.highlight .cm { color: #408080; font-style: italic } /* Comment.Multiline */
.highlight .cp { color: #BC7A00 } /* Comment.Preproc */
.highlight .cpf { color: #408080; font-style: italic } /* Comment.PreprocFile */
.highlight .c1 { color: #408080; font-style: italic } /* Comment.Single */
.highlight .cs { color: #408080; font-style: italic } /* Comment.Special */
.highlight .gd { color: #A00000 } /* Generic.Deleted */
.highlight .ge { font-style: italic } /* Generic.Emph */
.highlight .gr { color: #FF0000 } /* Generic.Error */
.highlight .gh { color: #000080; font-weight: bold } /* Generic.Heading */
.highlight .gi { color: #00A000 } /* Generic.Inserted */
.highlight .go { color: #888888 } /* Generic.Output */
.highlight .gp { color: #000080; font-weight: bold } /* Generic.Prompt */
.highlight .gs { font-weight: bold } /* Generic.Strong */
.highlight .gu { color: #800080; font-weight: bold } /* Generic.Subheading */
.highlight .gt { color: #0044DD } /* Generic.Traceback */
.highlight .kc { color: #008000; font-weight: bold } /* Keyword.Constant */
.highlight .kd { color: #008000; font-weight: bold } /* Keyword.Declaration */
.highlight .kn { color: #008000; font-weight: bold } /* Keyword.Namespace */
.highlight .kp { color: #008000 } /* Keyword.Pseudo */
.highlight .kr { color: #008000; font-weight: bold } /* Keyword.Reserved */
.highlight .kt { color: #B00040 } /* Keyword.Type */
.highlight .m { color: #666666 } /* Literal.Number */
.highlight .s { color: #BA2121 } /* Literal.String */
.highlight .na { color: #7D9029 } /* Name.Attribute */
.highlight .nb { color: #008000 } /* Name.Builtin */
.highlight .nc { color: #0000FF; font-weight: bold } /* Name.Class */
.highlight .no { color: #880000 } /* Name.Constant */
.highlight .nd { color: #AA22FF } /* Name.Decorator */
.highlight .ni { color: #999999; font-weight: bold } /* Name.Entity */
.highlight .ne { color: #D2413A; font-weight: bold } /* Name.Exception */
.highlight .nf { color: #0000FF } /* Name.Function */
.highlight .nl { color: #A0A000 } /* Name.Label */
.highlight .nn { color: #0000FF; font-weight: bold } /* Name.Namespace */
.highlight .nt { color: #008000; font-weight: bold } /* Name.Tag */
.highlight .nv { color: #19177C } /* Name.Variable */
.highlight .ow { color: #AA22FF; font-weight: bold } /* Operator.Word */
.highlight .w { color: #bbbbbb } /* Text.Whitespace */
.highlight .mb { color: #666666 } /* Literal.Number.Bin */
.highlight .mf { color: #666666 } /* Literal.Number.Float */
.highlight .mh { color: #666666 } /* Literal.Number.Hex */
.highlight .mi { color: #666666 } /* Literal.Number.Integer */
.highlight .mo { color: #666666 } /* Literal.Number.Oct */
.highlight .sa { color: #BA2121 } /* Literal.String.Affix */
.highlight .sb { color: #BA2121 } /* Literal.String.Backtick */
.highlight .sc { color: #BA2121 } /* Literal.String.Char */
.highlight .dl { color: #BA2121 } /* Literal.String.Delimiter */
.highlight .sd { color: #BA2121; font-style: italic } /* Literal.String.Doc */
.highlight .s2 { color: #BA2121 } /* Literal.String.Double */
.highlight .se { color: #BB6622; font-weight: bold } /* Literal.String.Escape */
.highlight .sh { color: #BA2121 } /* Literal.String.Heredoc */
.highlight .si { color: #BB6688; font-weight: bold } /* Literal.String.Interpol */
.highlight .sx { color: #008000 } /* Literal.String.Other */
.highlight .sr { color: #BB6688 } /* Literal.String.Regex */
.highlight .s1 { color: #BA2121 } /* Literal.String.Single */
.highlight .ss { color: #19177C } /* Literal.String.Symbol */
.highlight .bp { color: #008000 } /* Name.Builtin.Pseudo */
.highlight .fm { color: #0000FF } /* Name.Function.Magic */
.highlight .vc { color: #19177C } /* Name.Variable.Class */
.highlight .vg { color: #19177C } /* Name.Variable.Global */
.highlight .vi { color: #19177C } /* Name.Variable.Instance */
.highlight .vm { color: #19177C } /* Name.Variable.Magic */
.highlight .il { color: #666666 } /* Literal.Number.Integer.Long */
    </style>


<style type="text/css">
/* Overrides of notebook CSS for static HTML export */
body {
  overflow: visible;
  padding: 8px;
}

div#notebook {
  overflow: visible;
  border-top: none;
}@media print {
  div.cell {
    display: block;
    page-break-inside: avoid;
  }
  div.output_wrapper {
    display: block;
    page-break-inside: avoid;
  }
  div.output {
    display: block;
    page-break-inside: avoid;
  }
}
</style>

<!-- Loading mathjax macro -->
<!-- Load mathjax -->
    <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/latest.js?config=TeX-AMS_HTML"></script>
    <!-- MathJax configuration -->
    <script type="text/x-mathjax-config">
    MathJax.Hub.Config({
        tex2jax: {
            inlineMath: [ ['$','$'], ["\\(","\\)"] ],
            displayMath: [ ['$$','$$'], ["\\[","\\]"] ],
            processEscapes: true,
            processEnvironments: true
        },
        // Center justify equations in code and markdown cells. Elsewhere
        // we use CSS to left justify single line equations in code cells.
        displayAlign: 'center',
        "HTML-CSS": {
            styles: {'.MathJax_Display': {"margin": 0}},
            linebreaks: { automatic: true }
        }
    });
    </script>
    <!-- End of mathjax configuration -->

<style>
        .cell.nbinteract-left {
            width: 50%;
            float: left;
        }

        .cell.nbinteract-right {
            width: 50%;
            float: right;
        }

        .cell.nbinteract-hide_in > .input {
            display: none;
        }

        .cell.nbinteract-hide_out > .output_wrapper {
            display: none;
        }

        .cell:after {
          content: "";
          display: table;
          clear: both;
        }

        div.output_subarea {
            max-width: initial;
        }

        .jp-OutputPrompt {
            display: none;
        }
    </style></head>
<body>
  <div tabindex="-1" id="notebook" class="border-box-sizing">
    <div class="container">
      

  <div class="cell text_cell">
    <button class="js-nbinteract-widget">
      Loading widgets...
    </button>
  </div>


  <div class="nbinteract-hide_in
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="c1">#HIDDEN</span>
<span class="o">%</span><span class="k">matplotlib</span> inline

<span class="kn">from</span> <span class="nn">glob</span> <span class="k">import</span> <span class="n">glob</span>
<span class="kn">from</span> <span class="nn">IPython.display</span> <span class="k">import</span> <span class="n">Audio</span>
<span class="kn">from</span> <span class="nn">ipywidgets</span> <span class="k">import</span> <span class="n">Text</span><span class="p">,</span> <span class="n">Dropdown</span><span class="p">,</span> <span class="n">Output</span><span class="p">,</span> <span class="n">interact</span>
<span class="kn">from</span> <span class="nn">matplotlib.collections</span> <span class="k">import</span> <span class="n">LineCollection</span>
<span class="kn">from</span> <span class="nn">matplotlib</span> <span class="k">import</span> <span class="n">pyplot</span> <span class="k">as</span> <span class="n">plt</span>
<span class="kn">from</span> <span class="nn">pandas</span> <span class="k">import</span> <span class="n">DataFrame</span><span class="p">,</span> <span class="n">merge</span><span class="p">,</span> <span class="n">read_csv</span><span class="p">,</span> <span class="n">Series</span><span class="p">,</span> <span class="n">to_datetime</span>
<span class="kn">from</span> <span class="nn">pickle</span> <span class="k">import</span> <span class="n">dump</span><span class="p">,</span> <span class="n">load</span>
<span class="kn">from</span> <span class="nn">random</span> <span class="k">import</span> <span class="n">randint</span> 
<span class="kn">from</span> <span class="nn">sklearn</span> <span class="k">import</span> <span class="n">manifold</span>
<span class="kn">from</span> <span class="nn">sklearn.metrics</span> <span class="k">import</span> <span class="n">euclidean_distances</span>
<span class="kn">import</span> <span class="nn">cufflinks</span> <span class="k">as</span> <span class="nn">cf</span>
<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
<span class="kn">import</span> <span class="nn">warnings</span>
<span class="n">cf</span><span class="o">.</span><span class="n">go_offline</span><span class="p">()</span>
<span class="n">cf</span><span class="o">.</span><span class="n">set_config_file</span><span class="p">(</span><span class="n">offline</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">world_readable</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>

<span class="n">done</span> <span class="o">=</span> <span class="n">Audio</span><span class="p">(</span><span class="s1">&#39;done.wav&#39;</span><span class="p">,</span><span class="n">autoplay</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="n">warnings</span><span class="o">.</span><span class="n">simplefilter</span><span class="p">(</span><span class="n">action</span><span class="o">=</span><span class="s1">&#39;ignore&#39;</span><span class="p">,</span> <span class="n">category</span><span class="o">=</span><span class="ne">FutureWarning</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">comma</span><span class="p">(</span><span class="n">number</span><span class="p">):</span> <span class="k">return</span> <span class="s2">&quot;</span><span class="si">{:,}</span><span class="s2">&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">number</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">scolor</span><span class="p">(</span><span class="n">i</span><span class="p">,</span><span class="n">n</span><span class="p">,</span><span class="n">pickColor</span><span class="p">):</span> 
    <span class="n">scalar</span> <span class="o">=</span> <span class="mi">255</span> <span class="o">-</span> <span class="nb">int</span><span class="p">((</span><span class="n">i</span><span class="o">/</span><span class="nb">float</span><span class="p">(</span><span class="n">n</span><span class="p">))</span><span class="o">*</span><span class="mi">120</span><span class="p">)</span> 
    <span class="k">if</span> <span class="n">pickColor</span><span class="p">:</span> <span class="k">return</span> <span class="s1">&#39;#</span><span class="si">%02X%02X%02X</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="mi">128</span><span class="p">,</span><span class="n">scalar</span><span class="p">,</span><span class="mi">128</span><span class="p">)</span>
    <span class="k">return</span> <span class="s1">&#39;#</span><span class="si">%02X%02X%02X</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="mi">75</span><span class="p">,</span><span class="n">scalar</span><span class="p">,</span><span class="mi">200</span><span class="p">)</span>

<span class="c1">#conda install -n base bedtools samtools khmer numpy scipy sra-tools trimmomatic jupyterlab </span>
<span class="c1">#jupyter_contrib_nbextensions widgetsnbextension nodejs sra-tools r-essentials r-base r-rsqlite r-vegan bioconductor-biocinstaller </span>
</pre></div>

    </div>
</div>
</div>

<div class="output_wrapper">
<div class="output">


<div class="output_area">

    
<div class="output_html rendered_html output_subarea ">
        <script type="text/javascript">
        window.PlotlyConfig = {MathJaxConfig: 'local'};
        if (window.MathJax) {MathJax.Hub.Config({SVG: {font: "STIX-Web"}});}
        if (typeof require !== 'undefined') {
        require.undef("plotly");
        requirejs.config({
            paths: {
                'plotly': ['https://cdn.plot.ly/plotly-latest.min']
            }
        });
        require(['plotly'], function(Plotly) {
            window._Plotly = Plotly;
        });
        }
        </script>
        
</div>

</div>

</div>
</div>

  </div>
<div class="cell border-box-sizing text_cell rendered"><div class="inner_cell">
<div class="text_cell_render border-box-sizing rendered_html">
<h1><a id='outline'>Project Outline</a></h1><ul>
<li><a href="#seqSums">Sequencing Summaries</a><ul>
<li><a href="#readbd">Adapter Trimming and QC (Trimmomatic) Report</a></li>
<li><a href="#pAlign">Host Plant Alignment Report</a></li>
<li><a href="#swAlign">Switchgrass Fungal Alignments</a></li>
<li><a href="#aConc">Alignment Conclusions</a></li>
</ul>
</li>
<li><a href="#anno">Annotation Report</a>   </li>
</ul>
<ul>
<li><a href="#nmds">NMDS of annotated contigs</a><ul>
<li><a href="#anmds">All Crops</a></li>
<li><a href="#sgnmds">Switchgrass</a></li>
<li><a href="#msnmds">Miscanthus</a></li>
</ul>
</li>
<li><a href="#metaT">Function Analysis</a></li>
</ul>

</div>
</div>
</div>

  
  <div class="nbinteract-hide_in
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="c1">#HIDDEN</span>
<span class="c1"># For metaG</span>
<span class="n">metadataG</span> <span class="o">=</span> <span class="n">read_csv</span><span class="p">(</span><span class="s2">&quot;metadata/GLBRC_MetaG_Metadata.tsv&quot;</span><span class="p">,</span><span class="n">sep</span><span class="o">=</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
<span class="n">metadataG</span><span class="o">.</span><span class="n">set_index</span><span class="p">(</span><span class="s2">&quot;nucleic_acid_name&quot;</span><span class="p">,</span><span class="n">inplace</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="n">metadataG</span><span class="o">.</span><span class="n">drop</span><span class="p">([</span><span class="s2">&quot;source&quot;</span><span class="p">,</span><span class="s2">&quot;sampling ID&quot;</span><span class="p">,</span><span class="s2">&quot;sequencing_type&quot;</span><span class="p">,</span><span class="s2">&quot;height_mean_cm&quot;</span><span class="p">,</span><span class="s2">&quot;air_temp_c&quot;</span><span class="p">,</span><span class="s2">&quot;rep&quot;</span><span class="p">,</span><span class="s2">&quot;Sampling Time&quot;</span><span class="p">,</span><span class="s2">&quot;reads_file_name&quot;</span><span class="p">,</span><span class="s2">&quot;treatment&quot;</span><span class="p">],</span><span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span><span class="n">inplace</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span> 
<span class="k">for</span> <span class="nb">id</span> <span class="ow">in</span> <span class="n">metadataG</span><span class="o">.</span><span class="n">index</span><span class="p">:</span> <span class="n">metadataG</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="nb">id</span><span class="p">,</span><span class="s2">&quot;type&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="n">metadataG</span><span class="p">[</span><span class="n">metadataG</span><span class="o">.</span><span class="n">index</span> <span class="o">==</span> <span class="nb">id</span><span class="p">]</span><span class="o">.</span><span class="n">plot_name</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">0</span><span class="p">:</span><span class="mi">2</span><span class="p">]</span>
<span class="n">metadataG</span><span class="p">[</span><span class="s1">&#39;Date&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">to_datetime</span><span class="p">(</span><span class="n">metadataG</span><span class="o">.</span><span class="n">sampling_date</span><span class="p">)</span>
<span class="n">metadataG</span><span class="o">=</span><span class="n">metadataG</span><span class="o">.</span><span class="n">sort_values</span><span class="p">(</span><span class="n">by</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;type&quot;</span><span class="p">,</span><span class="s2">&quot;Date&quot;</span><span class="p">])</span>
<span class="n">metadataG</span><span class="o">.</span><span class="n">drop</span><span class="p">([</span><span class="s2">&quot;sampling_date&quot;</span><span class="p">],</span><span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span><span class="n">inplace</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="n">metaG_Reads</span> <span class="o">=</span> <span class="n">read_csv</span><span class="p">(</span><span class="s2">&quot;mapping/metaG/hostRemovalFlagstats/multiqc_data/multiqc_bowtie2.txt&quot;</span><span class="p">,</span><span class="n">sep</span><span class="o">=</span><span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">)</span>
<span class="k">for</span> <span class="nb">id</span> <span class="ow">in</span> <span class="n">metaG_Reads</span><span class="o">.</span><span class="n">index</span><span class="p">:</span> <span class="n">metaG_Reads</span><span class="o">.</span><span class="n">at</span><span class="p">[</span><span class="nb">id</span><span class="p">,</span><span class="s2">&quot;Sample&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="n">metaG_Reads</span><span class="o">.</span><span class="n">at</span><span class="p">[</span><span class="nb">id</span><span class="p">,</span><span class="s2">&quot;Sample&quot;</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;.stat&quot;</span><span class="p">,</span><span class="s2">&quot;&quot;</span><span class="p">)</span>
<span class="n">metaG_Reads</span><span class="o">.</span><span class="n">set_index</span><span class="p">(</span><span class="s2">&quot;Sample&quot;</span><span class="p">,</span><span class="n">inplace</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="n">metadataG</span> <span class="o">=</span> <span class="n">merge</span><span class="p">(</span><span class="n">metadataG</span><span class="p">,</span><span class="n">metaG_Reads</span><span class="p">,</span><span class="n">left_index</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span><span class="n">right_index</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="n">metadataG</span><span class="o">.</span><span class="n">sort_values</span><span class="p">(</span><span class="s2">&quot;Date&quot;</span><span class="p">,</span><span class="n">inplace</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="n">metadataG</span><span class="p">[</span><span class="s2">&quot;aligned&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span><span class="n">metadataG</span><span class="p">[</span><span class="s1">&#39;paired_total&#39;</span><span class="p">]</span><span class="o">-</span><span class="n">metadataG</span><span class="p">[</span><span class="s1">&#39;paired_aligned_mate_none_halved&#39;</span><span class="p">])</span>
<span class="n">metadataG</span><span class="p">[</span><span class="s2">&quot;percPlantAligned&quot;</span><span class="p">]</span><span class="o">=</span> <span class="n">metadataG</span><span class="p">[</span><span class="s2">&quot;overall_alignment_rate&quot;</span><span class="p">]</span>
<span class="n">metadataG</span><span class="p">[</span><span class="s2">&quot;Plant Reads&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="n">metadataG</span><span class="p">[</span><span class="s2">&quot;aligned&quot;</span><span class="p">]</span>
<span class="n">metadataG</span><span class="p">[</span><span class="s2">&quot;Total&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="n">metadataG</span><span class="p">[</span><span class="s2">&quot;paired_total&quot;</span><span class="p">]</span>
<span class="n">metadataG</span><span class="o">.</span><span class="n">drop</span><span class="p">([</span><span class="s1">&#39;aligned&#39;</span><span class="p">,</span><span class="s1">&#39;total_reads&#39;</span><span class="p">,</span><span class="s1">&#39;paired_total&#39;</span><span class="p">,</span><span class="s1">&#39;paired_aligned_none&#39;</span><span class="p">,</span><span class="s1">&#39;paired_total&#39;</span><span class="p">,</span><span class="s1">&#39;paired_aligned_one&#39;</span><span class="p">,</span> <span class="s1">&#39;paired_aligned_multi&#39;</span><span class="p">,</span>
       <span class="s1">&#39;paired_aligned_discord_one&#39;</span><span class="p">,</span> <span class="s1">&#39;paired_aligned_mate_none&#39;</span><span class="p">,</span>
       <span class="s1">&#39;paired_aligned_mate_one&#39;</span><span class="p">,</span> <span class="s1">&#39;paired_aligned_mate_multi&#39;</span><span class="p">,</span>
       <span class="s1">&#39;overall_alignment_rate&#39;</span><span class="p">,</span> <span class="s1">&#39;paired_aligned_mate_multi_halved&#39;</span><span class="p">,</span>
       <span class="s1">&#39;paired_aligned_mate_none_halved&#39;</span><span class="p">,</span> <span class="s1">&#39;paired_aligned_mate_one_halved&#39;</span><span class="p">],</span><span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span><span class="n">inplace</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="n">metaG_Reads</span> <span class="o">=</span> <span class="n">read_csv</span><span class="p">(</span><span class="s2">&quot;mapping/metaG/fungalRemovalFlagstats/multiqc_data/multiqc_bowtie2.txt&quot;</span><span class="p">,</span><span class="n">sep</span><span class="o">=</span><span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">)</span>
<span class="k">for</span> <span class="nb">id</span> <span class="ow">in</span> <span class="n">metaG_Reads</span><span class="o">.</span><span class="n">index</span><span class="p">:</span> <span class="n">metaG_Reads</span><span class="o">.</span><span class="n">at</span><span class="p">[</span><span class="nb">id</span><span class="p">,</span><span class="s2">&quot;Sample&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="n">metaG_Reads</span><span class="o">.</span><span class="n">at</span><span class="p">[</span><span class="nb">id</span><span class="p">,</span><span class="s2">&quot;Sample&quot;</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;.fungal.stat&quot;</span><span class="p">,</span><span class="s2">&quot;&quot;</span><span class="p">)</span>
<span class="n">metaG_Reads</span><span class="o">.</span><span class="n">set_index</span><span class="p">(</span><span class="s2">&quot;Sample&quot;</span><span class="p">,</span><span class="n">inplace</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="n">metadataG</span> <span class="o">=</span> <span class="n">merge</span><span class="p">(</span><span class="n">metadataG</span><span class="p">,</span><span class="n">metaG_Reads</span><span class="p">,</span><span class="n">left_index</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span><span class="n">right_index</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="n">metadataG</span><span class="o">.</span><span class="n">sort_values</span><span class="p">(</span><span class="s2">&quot;Date&quot;</span><span class="p">,</span><span class="n">inplace</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="n">metadataG</span><span class="p">[</span><span class="s2">&quot;Fungal Reads&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span><span class="n">metadataG</span><span class="p">[</span><span class="s1">&#39;paired_total&#39;</span><span class="p">]</span><span class="o">-</span><span class="n">metadataG</span><span class="p">[</span><span class="s1">&#39;paired_aligned_mate_none_halved&#39;</span><span class="p">])</span>
<span class="n">metadataG</span><span class="p">[</span><span class="s2">&quot;percFungalAligned&quot;</span><span class="p">]</span><span class="o">=</span> <span class="n">metadataG</span><span class="p">[</span><span class="s2">&quot;overall_alignment_rate&quot;</span><span class="p">]</span>
<span class="n">metadataG</span><span class="p">[</span><span class="s1">&#39;percFungalAligned&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">Series</span><span class="p">([</span><span class="nb">float</span><span class="p">(</span><span class="s2">&quot;</span><span class="si">{0:.2f}</span><span class="s2">%&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">val</span><span class="p">)</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;%&quot;</span><span class="p">,</span><span class="s2">&quot;&quot;</span><span class="p">))</span> <span class="k">for</span> <span class="n">val</span> <span class="ow">in</span> <span class="n">metadataG</span><span class="p">[</span><span class="s1">&#39;percFungalAligned&#39;</span><span class="p">]],</span> <span class="n">index</span> <span class="o">=</span> <span class="n">metadataG</span><span class="o">.</span><span class="n">index</span><span class="p">)</span>
<span class="n">metadataG</span><span class="p">[</span><span class="s1">&#39;percPlantAligned&#39;</span><span class="p">]</span>  <span class="o">=</span> <span class="n">Series</span><span class="p">([</span><span class="nb">float</span><span class="p">(</span><span class="s2">&quot;</span><span class="si">{0:.2f}</span><span class="s2">%&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">val</span><span class="p">)</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;%&quot;</span><span class="p">,</span><span class="s2">&quot;&quot;</span><span class="p">))</span> <span class="k">for</span> <span class="n">val</span> <span class="ow">in</span> <span class="n">metadataG</span><span class="p">[</span><span class="s1">&#39;percPlantAligned&#39;</span><span class="p">]],</span> <span class="n">index</span> <span class="o">=</span> <span class="n">metadataG</span><span class="o">.</span><span class="n">index</span><span class="p">)</span>
<span class="n">metadataG</span><span class="p">[</span><span class="s1">&#39;Remaining&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">metadataG</span><span class="p">[</span><span class="s1">&#39;paired_aligned_mate_none_halved&#39;</span><span class="p">]</span>
<span class="n">metadataG</span><span class="p">[</span><span class="s1">&#39;percRemaining&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span><span class="n">metadataG</span><span class="p">[</span><span class="s2">&quot;Remaining&quot;</span><span class="p">]</span><span class="o">/</span><span class="n">metadataG</span><span class="p">[</span><span class="s1">&#39;Total&#39;</span><span class="p">])</span><span class="o">*</span><span class="mi">100</span>

<span class="n">metadataG</span><span class="o">.</span><span class="n">drop</span><span class="p">([</span><span class="s1">&#39;total_reads&#39;</span><span class="p">,</span><span class="s1">&#39;paired_total&#39;</span><span class="p">,</span><span class="s1">&#39;paired_aligned_none&#39;</span><span class="p">,</span><span class="s1">&#39;paired_total&#39;</span><span class="p">,</span><span class="s1">&#39;paired_aligned_one&#39;</span><span class="p">,</span> <span class="s1">&#39;paired_aligned_multi&#39;</span><span class="p">,</span>
       <span class="s1">&#39;paired_aligned_discord_one&#39;</span><span class="p">,</span> <span class="s1">&#39;paired_aligned_mate_none&#39;</span><span class="p">,</span>
       <span class="s1">&#39;paired_aligned_mate_one&#39;</span><span class="p">,</span> <span class="s1">&#39;paired_aligned_mate_multi&#39;</span><span class="p">,</span>
       <span class="s1">&#39;overall_alignment_rate&#39;</span><span class="p">,</span> <span class="s1">&#39;paired_aligned_mate_multi_halved&#39;</span><span class="p">,</span>
       <span class="s1">&#39;paired_aligned_mate_none_halved&#39;</span><span class="p">,</span> <span class="s1">&#39;paired_aligned_mate_one_halved&#39;</span><span class="p">],</span><span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span><span class="n">inplace</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
</pre></div>

    </div>
</div>
</div>

  </div>
<div class="cell border-box-sizing text_cell rendered"><div class="inner_cell">
<div class="text_cell_render border-box-sizing rendered_html">
<h2 id="seqSums">Read QC and alignment</h2><h4 id="Adapter-trimming-and-QC">Adapter trimming and QC<a class="anchor-link" href="#Adapter-trimming-and-QC">&#182;</a></h4><p><img src="images/TrimReport.png" alt="alt text" title="Title"></p>

</div>
</div>
</div>
<div class="cell border-box-sizing text_cell rendered"><div class="inner_cell">
<div class="text_cell_render border-box-sizing rendered_html">
<h4 id='plantAlign'> When the reads are aligned to plant reference genomes, how many of the reads are plant-aligned reads?</h4><p><b><a href="scripts/hpc_scripts/NGS_Mapping.sh">Methodology</a></b></p><p><p>QC'd reads were aligned to their respective plant reference genome: </p>
    <ol>
        <li>bowtie2 paired-end alignment to respective reference assembly</li>
        <li>Report tables generated using <a href="https://multiqc.info/">multiqc</a></li>
        <li>Displayed below using pandas and nbinteract, two python libraries</li>
    </ol></p>

</div>
</div>
</div>

  
  <div class="nbinteract-hide_in
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="c1">#HIDDEN</span>

<span class="n">dataStr</span> <span class="o">=</span> <span class="s2">&quot;&quot;&quot;G5R2_MAIN_09MAY2016_LD1,G5R2_MAIN,G5,2016-05-09,43.02,2444885.5,5682372,230.5,0.01,3101297.5,54.57751622033897</span>
<span class="s2">G5R4_NF_09MAY2016_LD1,G5R4_NF,G5,2016-05-09,79.73,4575140.5,5737475,245.0,0.03,938323.0,16.354284768125353</span>
<span class="s2">G5R1_NF_09MAY2016_LD1,G5R1_NF,G5,2016-05-09,37.16,2034146.5,5473795,487.0,0.01,3333201.0,60.89378575558639</span>
<span class="s2">G5R2_NF_09MAY2016_LD1,G5R2_NF,G5,2016-05-09,61.07,4093313.5,6700488,383.5,0.02,2401160.5,35.83560630210815</span>
<span class="s2">G5R4_MAIN_09MAY2016_LD1,G5R4_MAIN,G5,2016-05-09,85.16,4535606.0,5324879,283.5,0.05,569866.5,10.701961490580349</span>
<span class="s2">G5R1_MAIN_09MAY2016_LD1,G5R1_MAIN,G5,2016-05-09,73.46,5016843.5,6828883,240.0,0.02,1572579.0,23.028348852952966</span>
<span class="s2">G5R3_NF_09MAY2016_LD1,G5R3_NF,G5,2016-05-09,80.7,5001844.0,6196018,199.5,0.02,949029.5,15.316764735028206</span>
<span class="s2">G6R1_MAIN_09MAY2016_LD1,G6R1_MAIN,G6,2016-05-09,85.88,5766456.0,6713739,39.0,0.01,559512.0,8.33383603384046</span>
<span class="s2">G5R3_MAIN_09MAY2016_LD1,G5R3_MAIN,G5,2016-05-09,84.41,4590265.0,5436507,272.5,0.04,625518.5,11.505889719262754</span>
<span class="s2">G6R3_MAIN_09MAY2016_LD1,G6R3_MAIN,G6,2016-05-09,86.34,6169902.0,7145090,63.0,0.01,564880.0,7.905848631717725</span>
<span class="s2">G6R1_NF_09MAY2016_LD1,G6R1_NF,G6,2016-05-09,86.57,6516872.5,7527497,52.5,0.01,571074.5,7.586512488812683</span>
<span class="s2">G6R2_MAIN_09MAY2016_LD1,G6R2_MAIN,G6,2016-05-09,86.06,5759999.0,6692593,115.5,0.02,549879.5,8.216239953632321</span>
<span class="s2">G6R4_NF_09MAY2016_LD1,G6R4_NF,G6,2016-05-09,86.98,5748471.0,6607949,88.5,0.02,480675.5,7.274201117472305</span>
<span class="s2">G6R2_NF_09MAY2016_LD1,G6R2_NF,G6,2016-05-09,86.22,11483052.5,13316083,228.5,0.02,1075775.5,8.078768358533061</span>
<span class="s2">G6R4_MAIN_09MAY2016_LD1,G6R4_MAIN,G6,2016-05-09,86.36,10680511.5,12361687,570.5,0.06,985639.5,7.973341340870384</span>
<span class="s2">G6R3_NF_09MAY2016_LD1,G6R3_NF,G6,2016-05-09,86.58,5920682.5,6837832,62.5,0.01,523727.5,7.65926246798693</span>
<span class="s2">G6R1_MAIN_31MAY2016_LD1,G6R1_MAIN,G6,2016-05-31,86.0,4589765.0,5336461,204.0,0.05,447497.0,8.385651089739062</span>
<span class="s2">G5R1_MAIN_31MAY2016_LD1,G5R1_MAIN,G5,2016-05-31,87.81,5542677.0,6310890,394.5,0.08,491297.5,7.784916232100385</span>
<span class="s2">G5R4_MAIN_31MAY2016_LD1,G5R4_MAIN,G5,2016-05-31,88.47,5921339.0,6691560,427.5,0.09,475789.5,7.1102926671807465</span>
<span class="s2">G5R4_NF_31MAY2016_LD1,G5R4_NF,G5,2016-05-31,87.97,5218316.5,5931777,626.5,0.14,456660.5,7.698544635106816</span>
<span class="s2">G5R2_MAIN_31MAY2016_LD1,G5R2_MAIN,G5,2016-05-31,88.29,10553216.5,11950005,619.0,0.07,879644.0,7.36103457697298</span>
<span class="s2">G5R1_NF_31MAY2016_LD1,G5R1_NF,G5,2016-05-31,87.65,6821004.0,7776723,938.0,0.16,601802.0,7.738503737371126</span>
<span class="s2">G5R2_NF_31MAY2016_LD1,G5R2_NF,G5,2016-05-31,88.12,8249743.5,9358299,439.0,0.06,674956.0,7.212379087267889</span>
<span class="s2">G5R3_NF_31MAY2016_LD1,G5R3_NF,G5,2016-05-31,87.5,5036978.0,5755740,714.0,0.15,474196.0,8.238662622008638</span>
<span class="s2">G6R2_NF_31MAY2016_LD1,G6R2_NF,G6,2016-05-31,86.3,6707432.0,7771064,210.0,0.03,628542.0,8.088236051073572</span>
<span class="s2">G6R3_MAIN_31MAY2016_LD1,G6R3_MAIN,G6,2016-05-31,85.16,5393305.5,6331750,557.0,0.09,589557.0,9.311122517471473</span>
<span class="s2">G6R1_NF_31MAY2016_LD1,G6R1_NF,G6,2016-05-31,85.65,5390104.5,6292542,689.5,0.13,545324.5,8.66620357877627</span>
<span class="s2">G6R4_MAIN_31MAY2016_LD1,G6R4_MAIN,G6,2016-05-31,84.24,5567014.5,6607123,572.0,0.08,676111.0,10.233062105851518</span>
<span class="s2">G6R2_MAIN_31MAY2016_LD1,G6R2_MAIN,G6,2016-05-31,85.91,5781888.5,6729977,440.5,0.07,603103.5,8.961449645370259</span>
<span class="s2">G6R4_NF_31MAY2016_LD1,G6R4_NF,G6,2016-05-31,85.77,6503491.5,7581116,545.5,0.08,699856.5,9.231576195378095</span>
<span class="s2">G5R3_MAIN_31MAY2016_LD1,G5R3_MAIN,G5,2016-05-31,88.3,5812968.5,6582349,242.0,0.05,471430.0,7.162032885220762</span>
<span class="s2">G6R3_NF_31MAY2016_LD1,G6R3_NF,G6,2016-05-31,85.55,4907993.0,5736908,393.5,0.08,502712.5,8.762777789011084</span>
<span class="s2">G6R3_NF_20JUN2016_LD1,G6R3_NF,G6,2016-06-20,84.6,5671552.0,6703466,2010.5,0.31,646680.5,9.64695726061712</span>
<span class="s2">G6R3_MAIN_20JUN2016_LD1,G6R3_MAIN,G6,2016-06-20,85.86,6135909.0,7145612,849.0,0.14,592992.0,8.298687362258123</span>
<span class="s2">G6R4_NF_20JUN2016_LD1,G6R4_NF,G6,2016-06-20,83.87,10446119.5,12452913,2776.5,0.19,1446949.5,11.619365685763643</span>
<span class="s2">G6R2_MAIN_20JUN2016_LD1,G6R2_MAIN,G6,2016-06-20,85.41,11384326.0,13325217,3304.0,0.28,1180202.0,8.856906420360735</span>
<span class="s2">G6R4_MAIN_20JUN2016_LD1,G6R4_MAIN,G6,2016-06-20,81.91,5485149.0,6695207,1731.5,0.2,851777.5,12.722198133679811</span>
<span class="s2">G6R2_NF_20JUN2016_LD1,G6R2_NF,G6,2016-06-20,85.47,5712932.0,6682956,2443.0,0.41,593585.0,8.882072543946123</span>
<span class="s2">G6R1_MAIN_20JUN2016_LD1,G6R1_MAIN,G6,2016-06-20,86.14,5177962.0,6010405,647.5,0.13,482787.5,8.032528590003503</span>
<span class="s2">G5R4_NF_20JUN2016_LD1,G5R4_NF,G5,2016-06-20,87.94,6100780.5,6936916,2196.0,0.41,537134.0,7.7431238896362595</span>
<span class="s2">G5R4_MAIN_20JUN2016_LD1,G5R4_MAIN,G5,2016-06-20,86.83,6715795.5,7732527,5536.0,0.81,680666.0,8.802633343536984</span>
<span class="s2">G5R3_NF_20JUN2016_LD1,G5R3_NF,G5,2016-06-20,81.38,5141417.0,6317596,1620.0,0.18,911401.0,14.426389405083833</span>
<span class="s2">G5R1_MAIN_20JUN2016_LD1,G5R1_MAIN,G5,2016-06-20,77.82,5013160.5,6441413,2211.5,0.19,1180776.5,18.33101681261549</span>
<span class="s2">G5R3_MAIN_20JUN2016_LD1,G5R3_MAIN,G5,2016-06-20,88.48,5700839.5,6442699,994.5,0.22,456179.5,7.080565148239891</span>
<span class="s2">G5R2_NF_20JUN2016_LD1,G5R2_NF,G5,2016-06-20,87.78,5487295.0,6249934,3378.0,0.68,493303.0,7.89293134935505</span>
<span class="s2">G5R2_MAIN_20JUN2016_LD1,G5R2_MAIN,G5,2016-06-20,88.04,5589304.5,6347927,2927.5,0.6,482960.5,7.608160900401028</span>
<span class="s2">G6R1_NF_20JUN2016_LD1,G6R1_NF,G6,2016-06-20,85.51,6103073.5,7136929,1316.0,0.21,616980.0,8.644894743943789</span>
<span class="s2">G5R1_NF_20JUN2016_LD1,G5R1_NF,G5,2016-06-20,86.61,5298116.5,6116500,3308.0,0.6,552031.0,9.025275893076106</span>
<span class="s2">G5R4_NF_12JUL2016_LD1,G5R4_NF,G5,2016-07-12,84.76,5476482.0,6460341,9528.5,1.35,695774.5,10.769934590140057</span>
<span class="s2">G5R2_NF_12JUL2016_LD1,G5R2_NF,G5,2016-07-12,87.96,5869056.5,6671812,4146.0,0.8,513375.0,7.694686241159074</span>
<span class="s2">G5R2_MAIN_12JUL2016_LD1,G5R2_MAIN,G5,2016-07-12,88.65,5987816.0,6753075,6761.5,1.44,464321.5,6.875704771530007</span>
<span class="s2">G5R1_MAIN_12JUL2016_LD1,G5R1_MAIN,G5,2016-07-12,88.09,8850117.0,10042351,8072.0,1.11,721231.0,7.18189396088625</span>
<span class="s2">G5R4_MAIN_12JUL2016_LD1,G5R4_MAIN,G5,2016-07-12,86.08,6006044.5,6976158,27967.0,4.09,655552.0,9.397034872203296</span>
<span class="s2">G5R3_NF_12JUL2016_LD1,G5R3_NF,G5,2016-07-12,87.92,5650799.0,6426349,3666.5,0.74,489209.5,7.6125573011985495</span>
<span class="s2">G5R1_NF_12JUL2016_LD1,G5R1_NF,G5,2016-07-12,87.65,5863094.0,6688179,15945.5,2.99,517994.5,7.744925786226714</span>
<span class="s2">G6R2_NF_12JUL2016_LD1,G6R2_NF,G6,2016-07-12,85.86,15344005.5,17866546,4512.5,0.3,1492239.5,8.352143161862399</span>
<span class="s2">G6R4_NF_12JUL2016_LD1,G6R4_NF,G6,2016-07-12,85.0,11963642.5,14071595,10343.0,0.8,1286317.0,9.141230969197165</span>
<span class="s2">G6R4_MAIN_12JUL2016_LD1,G6R4_MAIN,G6,2016-07-12,85.15,5534405.0,6499072,4525.5,0.76,588370.5,9.053146356895262</span>
<span class="s2">G6R1_NF_12JUL2016_LD1,G6R1_NF,G6,2016-07-12,85.63,5643997.5,6590819,2754.0,0.49,559495.0,8.48900569109848</span>
<span class="s2">G6R1_MAIN_12JUL2016_LD1,G6R1_MAIN,G6,2016-07-12,83.61,4497926.5,5378728,2752.0,0.49,562593.0,10.459591933260057</span>
<span class="s2">G6R3_MAIN_12JUL2016_LD1,G6R3_MAIN,G6,2016-07-12,86.07,5089800.0,5912717,2432.0,0.51,475522.0,8.042360221197802</span>
<span class="s2">G6R3_NF_12JUL2016_LD1,G6R3_NF,G6,2016-07-12,84.78,4832968.0,5700114,4311.0,0.8,533441.0,9.358426866550388</span>
<span class="s2">G5R3_MAIN_12JUL2016_LD1,G5R3_MAIN,G5,2016-07-12,88.14,5450573.0,6182923,4988.5,1.07,461855.5,7.46985689454648</span>
<span class="s2">G6R2_MAIN_12JUL2016_LD1,G6R2_MAIN,G6,2016-07-12,85.62,10251109.0,11970111,2263.0,0.22,1018829.0,8.511441539681629</span>
<span class="s2">G6R1_MAIN_01AUG2016_LD1,G6R1_MAIN,G6,2016-08-01,82.98,4695413.5,5657378,10126.5,1.59,627861.5,11.098100568850093</span>
<span class="s2">G5R3_NF_01AUG2016_LD1,G5R3_NF,G5,2016-08-01,82.23,4856813.5,5905510,24475.5,3.06,775344.5,13.12917089294574</span>
<span class="s2">G5R4_NF_01AUG2016_LD1,G5R4_NF,G5,2016-08-01,84.25,11083140.5,13151939,105331.5,6.98,1403094.5,10.668347077947974</span>
<span class="s2">G5R2_MAIN_01AUG2016_LD1,G5R2_MAIN,G5,2016-08-01,78.43,10000184.5,12746203,205100.5,9.13,2041289.5,16.01488302045715</span>
<span class="s2">G6R4_NF_01AUG2016_LD1,G6R4_NF,G6,2016-08-01,81.26,10655178.0,13108055,21298.5,1.23,1704468.5,13.003214435703846</span>
<span class="s2">G6R2_NF_01AUG2016_LD1,G6R2_NF,G6,2016-08-01,83.35,5351872.5,6419666,3630.5,0.52,701156.5,10.922009026637834</span>
<span class="s2">G6R2_MAIN_01AUG2016_LD1,G6R2_MAIN,G6,2016-08-01,82.29,5006352.5,6082749,8431.5,1.15,723326.5,11.89144086004535</span>
<span class="s2">G6R4_MAIN_01AUG2016_LD1,G6R4_MAIN,G6,2016-08-01,80.62,4765084.5,5908281,6744.0,0.83,809106.0,13.694440057945789</span>
<span class="s2">G5R1_MAIN_01AUG2016_LD1,G5R1_MAIN,G5,2016-08-01,82.4,4881644.5,5924069,65453.5,8.16,736542.5,12.433050661631388</span>
<span class="s2">G6R3_MAIN_01AUG2016_LD1,G6R3_MAIN,G6,2016-08-01,84.67,4607519.5,5440967,3466.5,0.67,510451.5,9.381631978286213</span>
<span class="s2">G5R2_NF_01AUG2016_LD1,G5R2_NF,G5,2016-08-01,84.58,13356404.5,15787307,140160.0,7.88,1639224.0,10.383176814133025</span>
<span class="s2">G5R4_MAIN_01AUG2016_LD1,G5R4_MAIN,G5,2016-08-01,80.67,5088918.0,6306715,71330.0,7.39,893281.0,14.163966502370887</span>
<span class="s2">G5R1_NF_01AUG2016_LD1,G5R1_NF,G5,2016-08-01,82.15,5200676.5,6329412,57607.5,6.64,809665.5,12.792112442672398</span>
<span class="s2">G6R1_NF_01AUG2016_LD1,G6R1_NF,G6,2016-08-01,84.32,4999734.5,5928912,5400.5,0.93,577330.5,9.737545438353614</span>
<span class="s2">G5R3_MAIN_01AUG2016_LD1,G5R3_MAIN,G5,2016-08-01,81.65,4948744.5,6060102,47449.0,5.51,814192.0,13.435285412687772</span>
<span class="s2">G6R3_NF_01AUG2016_LD1,G6R3_NF,G6,2016-08-01,77.96,4453617.0,5711239,7273.0,0.77,939309.0,16.44667645671981</span>
<span class="s2">G5R3_MAIN_22AUG2016_LD1,G5R3_MAIN,G5,2016-08-22,52.0,2735946.5,5255407,147876.0,6.21,2234480.0,42.5177345922019</span>
<span class="s2">G5R1_NF_22AUG2016_LD1,G5R1_NF,G5,2016-08-22,75.96,4626496.0,6088961,76749.0,6.23,1155024.0,18.96914760991243</span>
<span class="s2">G5R2_NF_22AUG2016_LD1,G5R2_NF,G5,2016-08-22,79.02,3729827.0,4718274,47488.5,5.86,763407.5,16.179804309796335</span>
<span class="s2">G5R4_NF_22AUG2016_LD1,G5R4_NF,G5,2016-08-22,78.15,9359890.0,11972027,163507.0,7.59,1990638.0,16.62740987804321</span>
<span class="s2">G5R2_MAIN_22AUG2016_LD1,G5R2_MAIN,G5,2016-08-22,69.45,9572001.5,13770800,326894.0,8.78,3395956.0,24.66055712086444</span>
<span class="s2">G6R1_MAIN_22AUG2016_LD1,G6R1_MAIN,G6,2016-08-22,80.3,4487068.5,5586492,7945.0,1.01,776060.0,13.891723106378745</span>
<span class="s2">G6R3_MAIN_22AUG2016_LD1,G6R3_MAIN,G6,2016-08-22,79.46,3760759.0,4730626,4235.0,0.59,712830.0,15.068407436986142</span>
<span class="s2">G5R1_MAIN_22AUG2016_LD1,G5R1_MAIN,G5,2016-08-22,73.38,7126087.5,9695253,147605.0,6.71,2051174.0,21.156477298735783</span>
<span class="s2">G6R3_NF_22AUG2016_LD1,G6R3_NF,G6,2016-08-22,79.41,7336045.0,9235360,11875.0,0.83,1411208.0,15.280487171046934</span>
<span class="s2">G6R1_NF_22AUG2016_LD1,G6R1_NF,G6,2016-08-22,81.46,7315217.5,8977689,8550.0,0.72,1184033.0,13.188616803277547</span>
<span class="s2">G6R2_NF_22AUG2016_LD1,G6R2_NF,G6,2016-08-22,80.98,7858611.0,9700669,9664.0,0.72,1332356.0,13.734681597733106</span>
<span class="s2">G6R2_MAIN_22AUG2016_LD1,G6R2_MAIN,G6,2016-08-22,79.22,8667328.5,10933944,17419.0,1.04,1662195.0,15.202153952864583</span>
<span class="s2">G6R4_MAIN_22AUG2016_LD1,G6R4_MAIN,G6,2016-08-22,78.0,9370495.5,12007829,15616.0,0.78,1987906.0,16.555082521578214</span>
<span class="s2">G5R3_NF_22AUG2016_LD1,G5R3_NF,G5,2016-08-22,60.95,3610024.5,5920203,188165.5,8.84,1940423.5,32.77630006944018</span>
<span class="s2">G5R4_MAIN_22AUG2016_LD1,G5R4_MAIN,G5,2016-08-22,62.04,3661130.5,5898471,193594.0,9.39,1867030.0,31.65277916938135</span>
<span class="s2">G6R4_NF_22AUG2016_LD1,G6R4_NF,G6,2016-08-22,80.3,8217143.0,10229978,10435.0,0.71,1465380.0,14.324370981051961</span>
<span class="s2">G5R2_NF_12SEP2016_LD1,G5R2_NF,G5,2016-09-12,57.81,5163234.0,8925694,110375.5,3.14,3405613.5,38.155167542154146</span>
<span class="s2">G5R2_MAIN_12SEP2016_LD1,G5R2_MAIN,G5,2016-09-12,65.95,6260428.0,9486264,166688.0,5.71,2754756.0,29.03941952279633</span>
<span class="s2">G5R1_MAIN_12SEP2016_LD1,G5R1_MAIN,G5,2016-09-12,42.27,3368118.5,7957864,248828.5,5.62,4178289.5,52.5051634458694</span>
<span class="s2">G5R4_NF_12SEP2016_LD1,G5R4_NF,G5,2016-09-12,52.3,3952036.0,7547720,178799.0,5.26,3220462.0,42.668011001997954</span>
<span class="s2">G5R1_NF_12SEP2016_LD1,G5R1_NF,G5,2016-09-12,61.53,5621047.5,9128071,197461.5,6.1,3041559.5,33.32094480860195</span>
<span class="s2">G6R2_MAIN_12SEP2016_LD1,G6R2_MAIN,G6,2016-09-12,78.51,7481589.5,9526453,14193.0,0.92,1534811.0,16.11104363817257</span>
<span class="s2">G5R3_MAIN_12SEP2016_LD1,G5R3_MAIN,G5,2016-09-12,55.23,4388447.0,7938601,161060.0,4.8,3191794.0,40.20600103217179</span>
<span class="s2">G5R3_NF_12SEP2016_LD1,G5R3_NF,G5,2016-09-12,47.96,3916354.5,8156444,102477.5,2.53,3944008.5,48.3545096367976</span>
<span class="s2">G6R2_NF_12SEP2016_LD1,G6R2_NF,G6,2016-09-12,80.18,7916339.0,9870656,15662.5,1.09,1416937.5,14.35504894507518</span>
<span class="s2">G6R1_MAIN_12SEP2016_LD1,G6R1_MAIN,G6,2016-09-12,77.05,6288105.5,8157259,7489.5,0.52,1445479.5,17.72016188280892</span>
<span class="s2">G6R3_NF_12SEP2016_LD1,G6R3_NF,G6,2016-09-12,79.43,6106488.5,7685321,10643.0,0.92,1148741.0,14.94720910161072</span>
<span class="s2">G6R4_MAIN_12SEP2016_LD1,G6R4_MAIN,G6,2016-09-12,69.66,6753666.0,9689783,17239.0,0.7,2434399.0,25.123359315683334</span>
<span class="s2">G6R3_MAIN_12SEP2016_LD1,G6R3_MAIN,G6,2016-09-12,73.95,5500075.5,7433032,19400.0,1.23,1554624.0,20.915072072876857</span>
<span class="s2">G6R1_NF_12SEP2016_LD1,G6R1_NF,G6,2016-09-12,72.38,6529576.0,9016718,14827.0,0.71,2073333.0,22.9943201062737</span>
<span class="s2">G6R4_NF_12SEP2016_LD1,G6R4_NF,G6,2016-09-12,79.05,7784763.0,9844371,14631.0,0.93,1554474.0,15.790485750689404</span>
<span class="s2">G5R4_MAIN_12SEP2016_LD1,G5R4_MAIN,G5,2016-09-12,35.27,2683194.5,7595791,150212.5,3.14,4630635.5,60.96317684359667</span>
<span class="s2">G5R1_MAIN_03OCT2016_LD1,G5R1_MAIN,G5,2016-10-03,19.82,1693715.0,8528146,79877.0,1.18,6673938.0,78.25778311018597</span>
<span class="s2">G5R2_NF_03OCT2016_LD1,G5R2_NF,G5,2016-10-03,29.27,2608174.0,8899698,76623.0,1.24,6085159.0,68.3748931705323</span>
<span class="s2">G5R2_MAIN_03OCT2016_LD1,G5R2_MAIN,G5,2016-10-03,23.52,2090804.0,8873165,84764.0,1.27,6589822.0,74.26687095303649</span>
<span class="s2">G5R4_MAIN_03OCT2016_LD1,G5R4_MAIN,G5,2016-10-03,24.99,2891414.5,11550331,81760.5,0.96,8431181.5,72.99515052858658</span>
<span class="s2">G5R3_MAIN_03OCT2016_LD1,G5R3_MAIN,G5,2016-10-03,16.95,1343183.5,7906366,59621.5,0.92,6434206.5,81.38007398089084</span>
<span class="s2">G5R1_NF_03OCT2016_LD1,G5R1_NF,G5,2016-10-03,32.84,2786797.5,8471997,80805.0,1.46,5468798.0,64.55146289593823</span>
<span class="s2">G5R3_NF_03OCT2016_LD1,G5R3_NF,G5,2016-10-03,55.85,5278523.5,9441689,50607.5,1.29,3857580.5,40.85689011785921</span>
<span class="s2">G5R4_NF_03OCT2016_LD1,G5R4_NF,G5,2016-10-03,10.73,842740.5,7838486,87026.0,1.25,6865762.0,87.59040967860375</span>
<span class="s2">G6R3_NF_03OCT2016_LD1,G6R3_NF,G6,2016-10-03,82.11,7555021.5,9198716,8543.0,0.76,1117304.0,12.146303897196088</span>
<span class="s2">G6R4_NF_03OCT2016_LD1,G6R4_NF,G6,2016-10-03,67.6,6157032.5,9101083,23241.5,0.92,2515567.5,27.640309400540573</span>
<span class="s2">G6R4_MAIN_03OCT2016_LD1,G6R4_MAIN,G6,2016-10-03,72.75,7814311.5,10735815,10646.0,0.44,2383477.0,22.201174293707556</span>
<span class="s2">G6R3_MAIN_03OCT2016_LD1,G6R3_MAIN,G6,2016-10-03,77.79,5921213.0,7608735,12459.5,0.97,1268258.5,16.668454085994583</span>
<span class="s2">G6R1_MAIN_03OCT2016_LD1,G6R1_MAIN,G6,2016-10-03,82.58,7837373.5,9488885,3797.5,0.33,1131924.5,11.92895161022607</span>
<span class="s2">G6R1_NF_03OCT2016_LD1,G6R1_NF,G6,2016-10-03,75.2,6498248.0,8637188,14738.0,0.84,1729924.0,20.02878714692791</span>
<span class="s2">G6R2_NF_03OCT2016_LD1,G6R2_NF,G6,2016-10-03,75.81,6956577.0,9172480,15094.0,0.85,1769670.0,19.293255477253698</span>
<span class="s2">G6R2_MAIN_03OCT2016_LD1,G6R2_MAIN,G6,2016-10-03,70.74,6526185.0,9219877,12187.0,0.54,2247638.0,24.378177713216783</span>
<span class="s2">G6R4_MAIN_07NOV2016_LD1,G6R4_MAIN,G6,2016-11-07,26.19,1990040.0,7583071,32984.0,0.6,5425824.0,71.55180269313053</span>
<span class="s2">G6R2_NF_07NOV2016_LD1,G6R2_NF,G6,2016-11-07,28.51,2105794.0,7370105,52325.0,1.02,5067900.0,68.76292807225948</span>
<span class="s2">G6R1_MAIN_07NOV2016_LD1,G6R1_MAIN,G6,2016-11-07,18.58,1286592.0,6905794,43214.0,0.78,5486478.0,79.44746107399091</span>
<span class="s2">G6R1_NF_07NOV2016_LD1,G6R1_NF,G6,2016-11-07,24.89,1710699.0,6858763,53420.0,1.06,4982370.0,72.642399219801</span>
<span class="s2">G6R3_MAIN_07NOV2016_LD1,G6R3_MAIN,G6,2016-11-07,51.38,4029039.5,7832562,33285.0,0.94,3519722.0,44.937046141479634</span>
<span class="s2">G6R2_MAIN_07NOV2016_LD1,G6R2_MAIN,G6,2016-11-07,52.97,4631958.5,8733100,29281.0,0.77,3762898.0,43.08776952055971</span>
<span class="s2">G6R4_NF_07NOV2016_LD1,G6R4_NF,G6,2016-11-07,30.18,2318829.5,7669227,54941.5,1.06,5137738.5,66.991608150339</span>
<span class="s2">G6R3_NF_07NOV2016_LD1,G6R3_NF,G6,2016-11-07,41.43,8686844.5,20875176,138953.0,1.2,11428845.0,54.7484964917182&quot;&quot;&quot;</span>

<span class="n">header</span> <span class="o">=</span> <span class="p">[</span><span class="s2">&quot;sample_id&quot;</span><span class="p">,</span><span class="s2">&quot;plot_name&quot;</span><span class="p">,</span><span class="s2">&quot;type&quot;</span><span class="p">,</span><span class="s2">&quot;Date&quot;</span><span class="p">,</span><span class="s2">&quot;percPlantAligned&quot;</span><span class="p">,</span><span class="s2">&quot;Plant Reads&quot;</span><span class="p">,</span><span class="s2">&quot;Total&quot;</span><span class="p">,</span><span class="s2">&quot;Fungal Reads&quot;</span><span class="p">,</span><span class="s2">&quot;percFungalAligned&quot;</span><span class="p">,</span><span class="s2">&quot;Remaining&quot;</span><span class="p">,</span><span class="s2">&quot;percRemaining&quot;</span><span class="p">]</span>
<span class="n">data</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">dataStr</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">&quot;</span><span class="se">\n</span><span class="s2">&quot;</span><span class="p">):</span>
    <span class="n">rec</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">&quot;,&quot;</span><span class="p">)</span>
    <span class="n">data</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">rec</span><span class="p">)</span>

<span class="n">metadataG</span><span class="o">=</span> <span class="n">DataFrame</span><span class="p">(</span><span class="n">data</span><span class="p">,</span><span class="n">columns</span><span class="o">=</span><span class="n">header</span><span class="p">)</span>
<span class="n">metadataG</span><span class="o">.</span><span class="n">set_index</span><span class="p">(</span><span class="s2">&quot;sample_id&quot;</span><span class="p">,</span><span class="n">inplace</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>

<span class="nd">@interact</span>
<span class="k">def</span> <span class="nf">graph</span><span class="p">(</span><span class="n">Host_Plant</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;Switchgrass &amp; Miscanthus&quot;</span><span class="p">,</span><span class="s2">&quot;Switchgrass&quot;</span><span class="p">,</span><span class="s2">&quot;Miscanthus&quot;</span><span class="p">],</span><span class="n">By</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;Percentage&quot;</span><span class="p">,</span><span class="s2">&quot;Count&quot;</span><span class="p">]):</span>
    <span class="n">G5Data</span> <span class="o">=</span> <span class="n">metadataG</span><span class="p">[</span><span class="n">metadataG</span><span class="p">[</span><span class="s1">&#39;type&#39;</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;G5&#39;</span><span class="p">]</span>
    <span class="n">G6Data</span> <span class="o">=</span> <span class="n">metadataG</span><span class="p">[</span><span class="n">metadataG</span><span class="p">[</span><span class="s1">&#39;type&#39;</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;G6&#39;</span><span class="p">]</span>
    <span class="k">if</span> <span class="n">By</span> <span class="o">==</span> <span class="s2">&quot;Percentage&quot;</span><span class="p">:</span>
        <span class="k">if</span> <span class="p">(</span><span class="n">Host_Plant</span> <span class="o">==</span> <span class="s2">&quot;Switchgrass &amp; Miscanthus&quot;</span><span class="p">):</span>
            <span class="n">ax</span> <span class="o">=</span> <span class="n">metadataG</span><span class="o">.</span><span class="n">groupby</span><span class="p">([</span><span class="s1">&#39;Date&#39;</span><span class="p">,</span><span class="s1">&#39;plot_name&#39;</span><span class="p">])</span><span class="o">.</span><span class="n">sum</span><span class="p">()[</span><span class="s1">&#39;percPlantAligned&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">unstack</span><span class="p">()</span><span class="o">.</span><span class="n">iplot</span><span class="p">(</span><span class="n">title</span><span class="o">=</span><span class="s2">&quot;% Reads Aligning to Respective Plant Host Assembly G5=Switchgrass G6=Miscanthus&quot;</span><span class="p">);</span>
        <span class="k">elif</span> <span class="n">Host_Plant</span> <span class="o">==</span> <span class="s2">&quot;Switchgrass&quot;</span><span class="p">:</span>
            <span class="n">ax</span> <span class="o">=</span> <span class="n">G5Data</span><span class="o">.</span><span class="n">groupby</span><span class="p">([</span><span class="s1">&#39;Date&#39;</span><span class="p">,</span><span class="s1">&#39;plot_name&#39;</span><span class="p">])</span><span class="o">.</span><span class="n">sum</span><span class="p">()[</span><span class="s1">&#39;percPlantAligned&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">unstack</span><span class="p">()</span><span class="o">.</span><span class="n">iplot</span><span class="p">(</span><span class="n">title</span><span class="o">=</span><span class="s2">&quot;% Reads Aligning to Switchgrass Assembly&quot;</span><span class="p">,</span><span class="n">fontsize</span><span class="o">=</span><span class="mi">12</span><span class="p">);</span>
        <span class="k">else</span><span class="p">:</span> <span class="c1"># &quot;Miscanthus&quot;:</span>
            <span class="n">ax</span> <span class="o">=</span> <span class="n">G6Data</span><span class="o">.</span><span class="n">groupby</span><span class="p">([</span><span class="s1">&#39;Date&#39;</span><span class="p">,</span><span class="s1">&#39;plot_name&#39;</span><span class="p">])</span><span class="o">.</span><span class="n">sum</span><span class="p">()[</span><span class="s1">&#39;percPlantAligned&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">unstack</span><span class="p">()</span><span class="o">.</span><span class="n">iplot</span><span class="p">(</span><span class="n">title</span><span class="o">=</span><span class="s2">&quot;% Reads Aligning to Micanthus Assembly&quot;</span><span class="p">,</span><span class="n">fontsize</span><span class="o">=</span><span class="mi">12</span><span class="p">);</span>
        <span class="n">ylim</span> <span class="o">=</span> <span class="mi">100</span>
        <span class="n">ylab</span> <span class="o">=</span> <span class="s2">&quot;% Reads&quot;</span>
    <span class="k">else</span><span class="p">:</span>
        <span class="n">colors</span> <span class="o">=</span> <span class="p">[</span><span class="s2">&quot;#74C476&quot;</span><span class="p">,</span> <span class="s2">&quot;#f26d07&quot;</span><span class="p">,</span><span class="s2">&quot;#794955&quot;</span><span class="p">]</span>
        <span class="k">if</span> <span class="p">(</span><span class="n">Host_Plant</span> <span class="o">==</span> <span class="s2">&quot;Switchgrass &amp; Miscanthus&quot;</span><span class="p">):</span>
            <span class="n">ax</span> <span class="o">=</span> <span class="n">metadataG</span><span class="o">.</span><span class="n">loc</span><span class="p">[:,[</span><span class="s1">&#39;Plant Reads&#39;</span><span class="p">,</span><span class="s1">&#39;Fungal Reads&#39;</span><span class="p">,</span> <span class="s1">&#39;Remaining&#39;</span><span class="p">]]</span><span class="o">.</span><span class="n">iplot</span><span class="p">(</span><span class="n">kind</span><span class="o">=</span><span class="s1">&#39;bar&#39;</span><span class="p">,</span> <span class="n">barmode</span> <span class="o">=</span> <span class="s1">&#39;stack&#39;</span><span class="p">,</span> <span class="n">color</span><span class="o">=</span><span class="n">colors</span><span class="p">,</span> <span class="n">title</span><span class="o">=</span><span class="s2">&quot;Reads Counts By Source&quot;</span><span class="p">)</span>
        <span class="k">elif</span> <span class="n">Host_Plant</span> <span class="o">==</span> <span class="s2">&quot;Switchgrass&quot;</span><span class="p">:</span>
            <span class="n">ax</span> <span class="o">=</span> <span class="n">G5Data</span><span class="o">.</span><span class="n">loc</span><span class="p">[:,[</span><span class="s1">&#39;Plant Reads&#39;</span><span class="p">,</span><span class="s1">&#39;Fungal Reads&#39;</span><span class="p">,</span> <span class="s1">&#39;Remaining&#39;</span><span class="p">]]</span><span class="o">.</span><span class="n">iplot</span><span class="p">(</span><span class="n">kind</span><span class="o">=</span><span class="s1">&#39;bar&#39;</span><span class="p">,</span> <span class="n">barmode</span> <span class="o">=</span> <span class="s1">&#39;stack&#39;</span><span class="p">,</span> <span class="n">color</span><span class="o">=</span><span class="n">colors</span><span class="p">,</span> <span class="n">title</span><span class="o">=</span><span class="s2">&quot;Switchgrass Reads Counts&quot;</span><span class="p">)</span>
        <span class="k">else</span><span class="p">:</span>
            <span class="n">ax</span> <span class="o">=</span> <span class="n">G5Data</span><span class="o">.</span><span class="n">loc</span><span class="p">[:,[</span><span class="s1">&#39;Plant Reads&#39;</span><span class="p">,</span><span class="s1">&#39;Fungal Reads&#39;</span><span class="p">,</span> <span class="s1">&#39;Remaining&#39;</span><span class="p">]]</span><span class="o">.</span><span class="n">iplot</span><span class="p">(</span><span class="n">kind</span><span class="o">=</span><span class="s1">&#39;bar&#39;</span><span class="p">,</span> <span class="n">barmode</span> <span class="o">=</span> <span class="s1">&#39;stack&#39;</span><span class="p">,</span> <span class="n">color</span><span class="o">=</span><span class="n">colors</span><span class="p">,</span> <span class="n">title</span><span class="o">=</span><span class="s2">&quot;Miscanthus Reads Counts By Source&quot;</span><span class="p">)</span>
    <span class="k">return</span> <span class="n">ax</span>
</pre></div>

    </div>
</div>
</div>

<div class="output_wrapper">
<div class="output">


<div class="output_area">

    
  <div class="output_subarea output_widget_view ">
    <button class="js-nbinteract-widget">
      Loading widgets...
    </button>
  </div>

</div>

</div>
</div>

  </div>
<div class="cell border-box-sizing text_cell rendered"><div class="inner_cell">
<div class="text_cell_render border-box-sizing rendered_html">
<h2 id="What-reads-are-fungal-reads?">What reads are fungal reads?<a class="anchor-link" href="#What-reads-are-fungal-reads?">&#182;</a></h2>
</div>
</div>
</div>

  
  <div class="nbinteract-hide_in
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="c1">#HIDDEN</span>
<span class="nd">@interact</span>
<span class="k">def</span> <span class="nf">fungalAlign</span><span class="p">(</span><span class="n">Samples</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;Switchgrass&quot;</span><span class="p">,</span> <span class="s2">&quot;Miscanthus&quot;</span><span class="p">,</span> <span class="s2">&quot;Switchgrass &amp; Miscanthus&quot;</span><span class="p">]):</span>
    <span class="k">if</span> <span class="n">Samples</span> <span class="o">==</span> <span class="s2">&quot;Switchgrass&quot;</span><span class="p">:</span>
        <span class="n">G5Data</span> <span class="o">=</span> <span class="n">metadataG</span><span class="p">[</span><span class="n">metadataG</span><span class="p">[</span><span class="s1">&#39;type&#39;</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;G5&#39;</span><span class="p">]</span>
        <span class="k">return</span> <span class="n">G5Data</span><span class="o">.</span><span class="n">groupby</span><span class="p">([</span><span class="s1">&#39;Date&#39;</span><span class="p">,</span><span class="s1">&#39;plot_name&#39;</span><span class="p">])</span><span class="o">.</span><span class="n">sum</span><span class="p">()[</span><span class="s1">&#39;percFungalAligned&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">unstack</span><span class="p">()</span><span class="o">.</span><span class="n">iplot</span><span class="p">(</span><span class="n">yTitle</span><span class="o">=</span><span class="s2">&quot;Percentage of Reads&quot;</span><span class="p">,</span><span class="n">title</span><span class="o">=</span><span class="s2">&quot;Switchgrass Samples Perctages of Reads Aligning to Combined Fungal Assemblies&quot;</span><span class="p">);</span>
    <span class="k">elif</span> <span class="n">Samples</span> <span class="o">==</span> <span class="s2">&quot;Miscanthus&quot;</span><span class="p">:</span>
        <span class="n">G6Data</span> <span class="o">=</span> <span class="n">metadataG</span><span class="p">[</span><span class="n">metadataG</span><span class="p">[</span><span class="s1">&#39;type&#39;</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;G6&#39;</span><span class="p">]</span>
        <span class="k">return</span> <span class="n">G6Data</span><span class="o">.</span><span class="n">groupby</span><span class="p">([</span><span class="s1">&#39;Date&#39;</span><span class="p">,</span><span class="s1">&#39;plot_name&#39;</span><span class="p">])</span><span class="o">.</span><span class="n">sum</span><span class="p">()[</span><span class="s1">&#39;percFungalAligned&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">unstack</span><span class="p">()</span><span class="o">.</span><span class="n">iplot</span><span class="p">(</span><span class="n">yTitle</span><span class="o">=</span><span class="s2">&quot;Percentage of Reads&quot;</span><span class="p">,</span><span class="n">title</span><span class="o">=</span><span class="s2">&quot;Miscanthus Samples Perctages of Reads Aligning to Combined Fungal Assemblies&quot;</span><span class="p">);</span>
    <span class="k">else</span><span class="p">:</span>
        <span class="k">return</span> <span class="n">metadataG</span><span class="o">.</span><span class="n">groupby</span><span class="p">([</span><span class="s1">&#39;Date&#39;</span><span class="p">,</span><span class="s1">&#39;plot_name&#39;</span><span class="p">])</span><span class="o">.</span><span class="n">sum</span><span class="p">()[</span><span class="s1">&#39;percFungalAligned&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">unstack</span><span class="p">()</span><span class="o">.</span><span class="n">iplot</span><span class="p">(</span><span class="n">yTitle</span><span class="o">=</span><span class="s2">&quot;Percentage of Reads&quot;</span><span class="p">,</span><span class="n">title</span><span class="o">=</span><span class="s2">&quot;All Samples Perctages of Reads Aligning to Combined Fungal Assemblies&quot;</span><span class="p">);</span>
</pre></div>

    </div>
</div>
</div>

<div class="output_wrapper">
<div class="output">


<div class="output_area">

    
  <div class="output_subarea output_widget_view ">
    <button class="js-nbinteract-widget">
      Loading widgets...
    </button>
  </div>

</div>

</div>
</div>

  </div>
<div class="cell border-box-sizing text_cell rendered"><div class="inner_cell">
<div class="text_cell_render border-box-sizing rendered_html">
<p><h2 id="anno">Assembly and MAGs</h2></p>
<p>The fittered reads (All-(plant+fungal)) were used to generate a metagenomic assembly. The assembly was then annotated with a set of prokaryotic peptides and a set of eukaryotic peptides. The diagram below shows numbers for contigs that had only prokayotic, both, and only eukarotic respectively.</p>
</div>
</div>
</div>

  
  <div class="nbinteract-hide_in
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="c1">#HIDDEN</span>
<span class="n">EukaryoticAnnotations</span><span class="p">,</span> <span class="n">ProkaryoticAnnotations</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(),</span> <span class="nb">set</span><span class="p">()</span>
<span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">open</span><span class="p">(</span><span class="s2">&quot;annotations/EukAnnotatedContigIDs2.txt&quot;</span><span class="p">):</span>  <span class="n">EukaryoticAnnotations</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">())</span>
<span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">open</span><span class="p">(</span><span class="s2">&quot;annotations/ProkAnnotatedContigIDs.txt&quot;</span><span class="p">):</span> <span class="n">ProkaryoticAnnotations</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">())</span>
<span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="k">as</span> <span class="nn">plt</span>
<span class="kn">from</span> <span class="nn">matplotlib_venn</span> <span class="k">import</span> <span class="n">venn2</span>
<span class="c1"># First way to call the 2 group Venn diagram:</span>
<span class="n">venn2</span><span class="p">(</span><span class="n">subsets</span> <span class="o">=</span> <span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">ProkaryoticAnnotations</span><span class="o">.</span><span class="n">difference</span><span class="p">(</span><span class="n">EukaryoticAnnotations</span><span class="p">)),</span> <span class="nb">len</span><span class="p">(</span><span class="n">ProkaryoticAnnotations</span><span class="o">.</span><span class="n">intersection</span><span class="p">(</span><span class="n">EukaryoticAnnotations</span><span class="p">)),</span> <span class="nb">len</span><span class="p">(</span><span class="n">EukaryoticAnnotations</span><span class="o">.</span><span class="n">difference</span><span class="p">(</span><span class="n">ProkaryoticAnnotations</span><span class="p">))),</span> <span class="n">set_labels</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;Prokaryotic Contigs&#39;</span><span class="p">,</span><span class="s1">&#39;Eukaryotic Contigs&#39;</span><span class="p">))</span>
<span class="n">plt</span><span class="o">.</span><span class="n">title</span><span class="p">(</span><span class="s1">&#39;Contigs with an Annotation&#39;</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">show</span><span class="p">()</span>
</pre></div>

    </div>
</div>
</div>

<div class="output_wrapper">
<div class="output">


<div class="output_area">

    
<div class="output_png output_subarea ">
<img src="data:image/png;base64,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
"
>
</div>

</div>

</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">EukaryoticContigIDs</span><span class="p">,</span> <span class="n">ProkaryoticContigIDs</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(),</span> <span class="nb">set</span><span class="p">()</span>
<span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">open</span><span class="p">(</span><span class="s2">&quot;annotations/EukAnnotatedContigIDs2.txt&quot;</span><span class="p">):</span>  <span class="n">EukaryoticContigIDs</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">())</span>
<span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">open</span><span class="p">(</span><span class="s2">&quot;annotations/ProkAnnotatedContigIDs.txt&quot;</span><span class="p">):</span> <span class="n">ProkaryoticContigIDs</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">())</span>
<span class="nb">len</span><span class="p">(</span><span class="n">EukaryoticContigIDs</span><span class="p">),</span> <span class="nb">len</span><span class="p">(</span><span class="n">ProkaryoticAnnotations</span><span class="p">)</span>
<span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="k">as</span> <span class="nn">plt</span>
<span class="kn">from</span> <span class="nn">matplotlib_venn</span> <span class="k">import</span> <span class="n">venn2</span>
<span class="c1"># First way to call the 2 group Venn diagram:</span>
<span class="n">venn2</span><span class="p">(</span><span class="n">subsets</span> <span class="o">=</span> <span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">ProkaryoticContigIDs</span><span class="o">.</span><span class="n">difference</span><span class="p">(</span><span class="n">EukaryoticContigIDs</span><span class="p">)),</span> 
                 <span class="nb">len</span><span class="p">(</span><span class="n">ProkaryoticContigIDs</span><span class="o">.</span><span class="n">intersection</span><span class="p">(</span><span class="n">EukaryoticContigIDs</span><span class="p">)),</span> 
                 <span class="nb">len</span><span class="p">(</span><span class="n">EukaryoticContigIDs</span><span class="o">.</span><span class="n">difference</span><span class="p">(</span><span class="n">ProkaryoticContigIDs</span><span class="p">))),</span> <span class="n">set_labels</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;Prokaryotic Contigs&#39;</span><span class="p">,</span><span class="s1">&#39;Eukaryotic Contigs&#39;</span><span class="p">))</span>
<span class="n">plt</span><span class="o">.</span><span class="n">title</span><span class="p">(</span><span class="s1">&#39;Contigs with an Annotation&#39;</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">show</span><span class="p">()</span>
</pre></div>

    </div>
</div>
</div>

<div class="output_wrapper">
<div class="output">


<div class="output_area">

    
<div class="output_png output_subarea ">
<img src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAUoAAAD5CAYAAABBAHxqAAAABHNCSVQICAgIfAhkiAAAAAlwSFlzAAALEgAACxIB0t1+/AAAADh0RVh0U29mdHdhcmUAbWF0cGxvdGxpYiB2ZXJzaW9uMy4xLjEsIGh0dHA6Ly9tYXRwbG90bGliLm9yZy8QZhcZAAAgAElEQVR4nO2deZwdZZW/n9N7d3rNvi8QCCGEENYAAkECioAwIjIsorjM4DLCqD9UBmiaRRFHBzfGUUEQEFkEVESEAAkEEvYkEEII2ZPuTtJJel9ud9/z++OtS27a7r6d7ltd91afJ5/6pG9V3apTb9361vuec973FVXFMAzD6JmMoA0wDMNIdUwoDcMwEmBCaRiGkQATSsMwjASYUBqGYSTAhNIwDCMBJpQhQ0RWicj8gM79dxH5XC/b7xaRmwfTpjAgIpeIyNNB2zGUMaEcBETkYhF5XUQaRaTKE5SPJOG4/yQ8qjpLVRcN9Nj9QVXPVNV7PNs+LyJLgrCjJ0RkmHcPnhzEc+5XOYjIVBFREcmKrVPV+1X1DH8sNPqCCaXPiMg3gduB7wNjgMnAHcC5Qdo1RPk00AacISLjgjbGSCNU1RafFqAEaAQu6GWfXJyQVnrL7UCut20+sBX4FrADqAIu97b9G9AORLxz/NVbvxFY4P2dD9wD7AFWA1cDW+PO/R1gG9AArAFO68a+aUAtkOF9/i2wI277fcBV3t+LgC8BM4FWoNOzrdbbfjfwS+Bv3jlfAQ7spWweBqqBOuAFYFbctv06lved54BbgDeBb3fZthH4NrDSO9+DQF6i+xB3n38P7AQ2AdfiKiE9lcNZwFtAPbAFuCHuWJsB9fZvBI4HPg8sidvnBOA1z87XgBPiti0CbgJe8srlaWBk0M9Cui+BGxDmBfg40AFk9bLPjcAyYDQwCngZuMnbNt/7/o1ANvAJoBko87bfDdzc5Xgb2SuUtwKLgTJgoicCW71tM7yHdLz3eWpPQuM9vEd5f68B1gMz47bN9f5eBHzJ+3ufhzvO3t3AsUAWcD/wx17K5gtAEXtfJssHcKzJQBQ4FCd4K7spt1eB8cBw3Ivlij7eh98Df/ZsnQq8D3yxl3KYD8zGienhwHbgvLj7oPG/mfhjeLbtAT7rXfdF3ucRcfdgHXAw7kW5CLg16Gch3RdrevvLCKBGVTt62ecS4EZV3aGqO4EK3EMQo93b3q6qT+JqGTP6eP7PAN9X1T2quhX4Wdy2TpwAHSoi2aq6UVXX9XCcxcApIjLW+/yI93kaUAys6KM9AI+q6qtemdwPHNHTjqp6l6o2qGobcAMwR0RK+nMs4DKcOL4LPADMEpG5Xfb5mapWqupu4K9djtftfRCRTOBC4HuerRuBH7PvPex6XYtU9W1VjarqSs+eU3qxPZ6zgLWqeq+qdqjqA8B7wDlx+/xOVd9X1RbgIXovF6MPmFD6yy5gZLxjvhvG45prMTZ56z48RhehbQYK+3j+8bhaY4wP/1bVD4CrcAK0Q0T+KCLj6Z7FuFrQybgm8CLcg30K8KKqRvtoD7imdIwer0VEMkXkVhFZJyL1uBofwMj9PZbHZTgxRVUrcdfUNULf2/F6ug8jgRz++R5O6MkQETlORJ4XkZ0iUgdc0eW6eqPr76W78+1PuRh9wITSX5bifFTn9bJPJTAl7vNkb11fSDT0UxWuyR1j0j5fVv2Dqn7EO78CP+zhOIuBk3BiuRhYApyIE8rF/bQtERfjAl4LcD7Aqd562d8DicgJwEHA90SkWkSqgeOAixK8xPpCDa622fUebvP+7q4c/gD8BZikqiXAr9h7XYnKrevvpev5DB8wofQRVa0Drgd+KSLniUiBiGSLyJkicpu32wPAtSIySkRGevvf18dTbAcO6GX7QzhxKBORCcDXYxtEZIaIfFREcnFi3oJrjnd3HWu97ZcCL6hqvXfu8+lZKLcDE0Ukp4/X0pUiXIR6F1CAyxroL58DnsH5J4/wlsO84545gOOiqp24cr5FRIpEZArwTfbew+7KoQjYraqtInIs7qUQYyfOl9rTfX0SONhLOcsSkQu963piINdh9I4Jpc+o6k9wD861uIdgC06wHvd2uRl4HRdoeRsXke1rUvadOB9jrYg83s32G3HR2g3AQpxvsc3blosL9tTgmmqjgWt6OddiXPNzc9xnwUVvu+M5YBVQLSI1fbyeeH6Pa1JuA97FBbz2GxHJw/lqf66q1XHLBuBe/rn53R/+A2jCBbmW4GqMd3nbuiuHrwI3ikgD7sX4UOxAqtqMi8y/5N3XefEnUtVdwNm4gNQuXCbD2aranzI2+oio2sC9QwUR+Qrwr6ra18CBYRhYjTLUiMg4ETlRRDJEZAauFvJY0HYZRroxUEe2kdrkAP/H3qTxP+J6BRmGsR9Y09swDCMB1vQ2DMNIgAmlYRhGAkwoDcMwEmBCaRiGkQATSsMwjASYUBqGYSTAhNIwDCMBJpSGYRgJMKE0DMNIgAmlYRhGAkwoDcMwEmBCaRiGkQATSsMwjASYUBqGYSTAhNIwDCMBJpSGYRgJMKE0DMNIgAmlYRhGAkwoDcMwEmBCaRiGkQCbhdEw+oFUiACZuMqGxG1SoF3Lbda+MGGzMBpGHJ4AFgHFQIn3fz6QB+R6/+cB2QkO1Q5E4pZWoBFo8JZGoEHLtTX5V2EkGxNKY8giFZILjIpbhgOFDK5LqhXYBdTE/V9nNdLUwoQyLIhkAaW4GlC2t+Tg3Cs57G0ixpqJgmsmtgDNQJP3v/tbtXMwzR8MpEIKgYnAeJwwlgRrUY90ANXANqASqDHhDBYTynRDJB8ow4li/FKY5DO1ES+crqm4A9iOaluSz+ULUiGZwDhgkreUBmtRv2kDqoCtwEYt1+aA7RlymFCmMiK5uAd8PHvFMTdQmxx7cDWe7UA1qvUB2/MhUiEZuDKbDkwhfAFLxZX9emCDiebgYEKZaogMByZ7yxj2jaimKs3ECyfsQjU6mAZIhYzDieMBpMbLZDBQXJm/D3yg5doRsD2hxYQyaJxvcTx7xTHZTeggaAXWAe+jutOvk0iF5AAzgFk43+xQJgKsBVZrue4O2piwYUIZBCKZuNrPNJxIhq15GM8eXI1nLZqcZqJUSClwGHAQidN0hiLVwCpgvQWBkoMJ5WAiUoCr/czE5eINJRQXjFgDbOpPVF0qZDRwFM4HaSSmDlgOrNXywXWFhA0TysFAZCQwGzgQ6zYKrpm4DliD6o5EO0uFjAKOxgSyvzTiBHONlocv7WswMKH0CxEBpuIEcmywxqQ0VcAbqFZ23SAVMgInkFMG3apw0gS8DrxvTfL9w4Qy2ciHAYbDcF3hjL5RBbyOapVUSAFwLHBwwDaFld3AUi3XbUEbki6YUCYLkQzgUJwPbaikpySVqKCvzWPLF09i+KqCUET/U52NOMFsCNqQVMeEMhmITAKOJ317fgTO7pG0vXU80lJIDsCKAlp+OYasqhyLavtMJ645vtKa4z1jQjkQREpxAmlBhn7Snk3n20fTVjmFfGTf5PoOiD5RRsvvR5LfnmFBMJ/ZASzWct0TtCGpiAllf3DN7LnAEbgxCY1+UDWRlhXHkd2R03se6a5MIj8fS/SNwiGXUjXYdAJvAissnWhfTCj3F5GxwMlYM3tArJpL04ZDGLY/33l9GM0/HUtObVaoE/RTgRpgoZanTh/+oDGh7Csumj0POCRoU9KZSA6dr51MZM8o8vvz/Wah8/ZxRJYW9e/7Rp+J4JriG4I2JBUwoewLzhd5BlaLHBC1ZbS9dgoZbfkDD9AsKqL5Z2PJM9+l77wDLBvqTXETykSITAPmY32KB8SmA2l+5yjyNDN5wrYji8jNE2BDnouUG76xA9cUbwzakKAwoewJ17PmGFzAxugnUUFXzKNl21QK/Dh+B0TvGk3rX8v8Ob7xIc3AU1quNUEbEgQmlN3hBsw9DTdtgNFPWvPpWHYqHY0l/kerny2m+adjyVdJi/E705UO4Fkt101BGzLYmFB2xQ2cewY2vuGA2D2StldPITNR6k8yeT+PlusmktOcaSlbPqLAy1quq4I2ZDAxoYxHZDou9cfSTwbAnhG0Lf0oWdGswResXZlErpsEW3LNb+kzK7VclwVtxGBhQhlDZB5weNBmpDu1w2l7+bRgRDJGq9B5/UQ6VhdYn3ufeVfLdUnQRgwGJpQAIh/BDWhhDIDaMtqWLiCrM0CRjBERojdPIPLWMOvN4zOrtVxfDNoIvzGhFDkBNySaMQDqSom8vIDMzuzgRTJGB0RvG0+bJaf7zntari8EbYSfDG2hFDkOmBO0GelOfQmRlxeQMZiBm77SCfrzsbQ8W2LpQz4TarEcur0aRI7GRHLANBSnrkgCZIJ8o5r8U+uw+a/95RCpkOOCNsIvhqZQihwJHBm0GelOYxGRl05PXZGMkQFyZTX5xzTSErQtIWeOVMisoI3wg6EnlCJzcPOwGAOgaRjt6SCSMTJBvreN3JnNtAVtS8g5QSpkatBGJJuhJZQihwGhbR4MFp0ZRF85lWh7bnqIZIxsyLhxK1lT2ogEbUuIEeA0qZAxQRuSTIaOUIocApwQtBlhYMU8WpuL0jNHMU/J/MFmMoZ30BG0LSEmE/iYVEho5j0aGkIpMhr4SNBmhIHNB9BcOSW9I8hFUbJu3kJndpQhPXSYz+QBp0uFhEJjQnERveIG3D2NoXCtPtNQTOSdo8ORwD0pQu63qmgN2o6QM4qQtOKGgnjMx+bXHjAdmURfPQWiSRxPMmhObKTgU7ssbchnDpUKOShoIwZKaH703eKCN1ODNiMMLD+e1thUsmHishry5zRZzdJnTpIKGR60EQMhvEIpMgo3x40xQDZOp7l6Unr7JXsiE+S7lWQVdtIZtC0hJgv4aDr7K9PW8F5xfskFhPX6BpH6EiKrjgyHX7InCqNkXV1p+ZU+Mxw4Kmgj+ktYhWQ+5pccMB2ZRF+dD8mc5yZVmdtMwZl7zF/pM3OkQkYFbUR/CN8DYH7JpLHqKFpaC8Lnl+yJL+4kd0yE9qDtCDEZwHypkJQZYaqvhEsoRUZgfsmkUF9CZMu0cPoleyJXybx2G52iDOEhtXynjDRsgodLKOEkwndNgbD8eKJkDL2JuqZGyDt3jw2e4TOHS4WUBW3E/hAeURGZAYwO2owwsPkAmuvLwh3A6Y1La8gttS6OfpIBnBi0EftDOITSRbmPDdqMMNCRRfTduUPHL9kduUrmf1TbwBk+M14q5ICgjegr4RBKN2yaDfefBN47nJZ0GTrNT45tomBWsyWi+8xx6RLYSX+hFCnDJgZLCq35dGyabi+cGN+oRiyw4ytFwOygjegL6S+UcAzhuI7AWTWXyFDImewr49vJXVBngR2fmSMVkh20EYlI74dCZAyWM5kUGoqJVE2y2mRXLqkhy2qVvpJLGsyCmt5CaaOVJ413jqJzKKYDJWJEJzkfr7Vapc/MTvVaZfoKpchkYGzQZoSBhmIiu8ZabbInLt5FdqbVKv0kD0jpScnSVyhtgrCksW6mddvrjdJOss+2JHS/OVwqJGWzLdJTKN3UDiODNiMMdGQSrZo8dJPL+8r5u8k2X6Wv5AGHBG1ET6SnUFo6UNLYOo3WzizSIpctSMo6yT6h0fIqfSZln+v0E0rXCydtMvpTnY0Hm0j2lU/vsmCXz5RKhYwP2ojuSD+hhIPBeo4kg9rhtDWWpOe0s0EwvY08mxPcd1IyqJOOQjkzaAPCwrqZNl3r/nLhLhssw2emSIUMC9qIrqSXUIqMw41nZwyQ9mw6qydYbXJ/mddAXoHNr+MnGaRgUCe9hNJqk0lj03TarLvi/pMNGafU2/w6PnNg0AZ0JX0eFJE8LIiTNDZNNz9vf1lQn0bPTXpSKhUyImgj4kmnGz6D9LI3Zdk1KpxzdA8W01vJHW4D+/pNStUq00l4Us5vka5UTrYgzkDIADmtzqLfPmNCud+IlAAlQZsRFmrGWrN7oJxab/mnPlMkFZIyU7ukh1DChKANCAvt2XQ2FZHSI7WkA5Mi1vweBKYEbUCMdBHKlMzWT0d2jCOCWA+TZHBcgzW/fSZlKkipL5Qiggll0tg+wQZ2SBbzGoO2IPSMkgpJiaBj6gsljAAb3SZZ7B5tze5kcUgLuTaikK8IKVKrTAehTImCCgPNBbS3FphQJosCJfPgVmt++0xKPP8mlEOIHRMs+JBs5jVamfrMxKANgFQXSpEMbLqHpLF9vDUTk82hzSn+DKU/xVIhgY9JkOo3eQw2pFrS2DPSeuMkmykRc2UMAqOCNiDVhdKa3UmivoRIR469dJLNsChZo9ptziGfCXzal1QXSmt2J4m64TY0mF8c2mJ+Sp+xGmUCioM2ICw0FVn/br84tMXK1mesRtkjLpCTciMdpytNhdYbxy+mt6bwcxQOioJOPE/lG1wI9nAni+bClL7Xac2odvP9DgKBti5T+eGxZncSaS2w0W78oriTrEzroeM3JpQ9UBS0AWFBQdtyrdbjF5kgo9stoOMzgeqBCeUQoKWADjLMjeEnEyKWVeAzVqPsARPKJNFUbA+x30yIWOTbZ6xG2QMmlEmi0VKDfGdsu/kofaYwyJOnslBaMCdJNBXZQ+w3RZ3m2vAZSw/6J0SysTEok0ZTkT3EflNkzg2/CXRgjNQUSks0TyqR3JS9z6GhMGovI5/JlAoJLHMjVR8gy/lLIlErTd8Z1pmyz1KYCKz5naq5dUn/0b0AZZ+FyxvdtLd6OrzwR3jum3DUPXDObhj7G/jBl2ATQB1kngqXboYpAno1PPj/4H2AyfCtRijJwo0a8w+4fS40APwnHPV7OAdgAmxZCXc+B8Mvgq8oZHRC5lnw3O/hBYCr4Oj74RNRyDgc3n4e/pTsa1efJxO76ik+t6We2bmZNPzhfCoAbljEOat28JHcLBoBzjyIxy6ZzTvLqxlRvoiKohy2A4wpZP2Pz+B+gMv/zLda2inJynDlWnEqtx9YRsN3FvKZbfXMAOiIktPWSdFjF3JV7PzbG8n7+pNUTC1j+Y9O5wGAZ9Yx+e7lfL5DyZlSwtu3LuDBDB9LoSDqs1BupIzHuJyI+/1yAC9wAc99uP1BTmc1n+YrfIsxNLKasTzJ52hkMofwOBfyzIf7LmIWy7gQJYOpLOEingJgHSN4jC/TwTCK2MwXuYs8OrmLz1Djyp8oObRTxHVcxQaG8whfQclAyeRgnuNf3O/aJ3KBZh+P3yOpKpRJrwPlQvQGeORy2LwJco+Aax+G1SfCtpPhf78Bl8bv/1U4CaAGbnwLij4O37gKvp+NC4zcBnfGRDXGEzD6fjjzZbhtBjS/5UXuj4K69+CHZdCxBXJnQflSWFEMHXfC+UvgljnQOBc+/wM45HvwXjKvPepzXWf+VF4uzOH5u97i8vj1R45j4fdOintAPYZls/O+T3FTd8f6wlzuPOPAfcv1hwt4KPb3j17m1G31TI7f/uOlnDum0L3EYty7kksuns19Zx7E+n9/gm/88R1mXTybVf25vr6QrT43vbOIMp9HmMtmasnlV1zLKlYziyo2UkYVh5LD7g/3L6WJ+fyRVczd5zgdCEu5iAu4nYns4WdcwypWMIsqnuJ8ZrGQM3md33AJT/IRPsVivrC3/HmEU9nllf846vg6PySfDurI5ZeUczQrmESdb6UQEKnaXEi6XcdB3eWwGWAKtI2Gqveh9HyoPg9Xu4lnPYyb5wnWXGjIh+a7Eswz/GM46WxYNMN768VqmSXQWYbruVEPWer1YX8ZRo6EHXNwta55sPovcGQyrxv8r1GedwhrRxbQ5Oc5Yryzg2OPn8Srsc/PrGNyUzvFh4zk3di6NTWUtEfJO+tg1mcIHD2epa9XdhGMJOO7g3Iidcx1v19KaWMYVeyiFIAn+Ayn8ieIy24YRwNHsYmMLjm0bzKNfHYynRry6GQSr7GSOUSBPcxgAW8CMIelbOaIf7JjE8cy0yv/PDrJ93oktZGF/8UQmB94yAhlPAthRCVMuhg29LTPDNi6GOY0Q8bTMKIKpqyFstj278LnRsN1Z8NZsV9iFYzeAGMmwtXj4bsVMCu2/wtQNgquPwJu/ST843ioOxl27oSxC2FEM2Qsgrm74s6RLDSgu/xWNade8ijXX/UUn9taT0FsfXM7Iy99lGsv/zPf/vN7TI//zj3L+dylj3JdxWLOinZJalq5neFNEUb8yyHuBdYRRf7wDhd85Wgeid9vUx2lBdnUxj6PHcaexognKj4hftco41nPCBqYxGw2sJDDyaeWOWzt03f3UEpBXM2ziD00UcZOCsmkhWwv53Y0e2jrUmYbGE4rIzghrsWzkTJu43p+xa3M4B8+1iYhQL1K1aa3b2yB3EvgiivgoWnQ2tN+d8BLH4dxU+G/ymDXJFiXjfsRPQB3ngi1myD3VLjiazDvV7CsEzKrYPRq+PFSKP0UXH0x3HAQtJwMe3bCjUuh5FPw1TfgjaOg4Uq4/zL4soBOh3XbU2CQ0mRw6eEsmlzCExkCFYs4979f5oLbP84904dT97Mz+e7kEpqeWcfkX7/JV+dN5IYxhbRefQJ3zhxF7Y4mcq95liv+93Xmfe0YlsWO+dc1HDOtjDdzMl3N6fZlnDJ9OG8fNpo9izbuPbd2kzUqEpJc0jpy+RNXcDQPkU2U5XyCL/DTPn+/O0EXuh/So2uZvcIxjOVNsuLWT2UPV3MjWyjhQb5KJW8w3rWkwkSq1ih96UnSAJmnwBUnwys/grd627cAoi/AQzvgpjVwRwsUHAk7AE7E1VamQNsCeHUlTAMYDntOhuVF0HkG7BoJ1YtgdPxxj4e6cVD5BzgI4BZYWQm3boMfToPt47xzJBMJoF/O9OE05GSiWRno+Yfy4o4mpgIU5tAxucQ1008/kM2FOexcsZ0xADNHuXIdPYy2I8by6sZaV64xVtdwzClT9ja7N9Vx4PJqTv3Mw3z/uQ18+oPdzPuv5/iXqaXUNrfvrQ1VN1E2LNvXmg46GELcRia/4wqm8Apn8BYbGEUrI/kV1/F9vk+EMu7kv9jWS2eN4eyhmeEffm6gjAJqGU0jneTT7mnCDsrI6VJmWziGw/aW/z5Moo4iKnnb/a59IrAeZqkqlElP3+0EToLLJkDVw7Aw0f7VkFPppSPcAjMzoPMCqGqGjLe97lQNkLkEDp8O2wA+Actfw0UH34bCXTDmBKh5EUp34CahWgMFG2D60Z5fNBbwWQMFT8L8/4QXk33tEsAQYGtqKIn9/Y8POKIsn0qADXsojHi9WN6sYmRjG6NnjmRnWwcZG2tduba0k/nuTg4fV+jKFWDZVsZEOin4xEGsj637+Znc+fAFfO+hC7jmo9N4ZPpwlt3yUR6bMZK6rAzanlzLtKjC65Ucf9R4lvt5vb4XcBT4HZdRTBWf8X6/s9nGtXyba7x/Oezhi9zCBOp7PM5cNtLCaNYxglYy2cIxzGYFGUAZa1jo+chXcDyT48rsPcbQTgHH7C1/NlFKkze5Wg0F7GE64//Z359EAmsVpGrTO+lvjl/A9BUwbyRsGw3XAXwFHmuBrDvgohYo/Ab8x/dhy3r46TtQ9Bm4UkCLofYeuAugFrIWwJVRyIxCxkxY/WtP3K6FVc/CoSPgBoHoF+CRWdB0C8z8FFyAu9FyLjx9kSeul8GFld7cxZfCE5/0oUaZ4fN7+OtP8qXqRg6OdFJ4wcP88KTJ/OWD3czY1cxEBApz2PXNedwH8PxGDlq4nnNF6BSIfnIG908qoXlXMznXPc+VUSVTlYyJxaz++rF7XxpPfcCxB43gtb6m+Hz2cO6/ezmfv2cF2ZNLWHXRYbzjz9U72v2uUb7KdKqZRwHbuM39fjmGxzi1h+vaRjF38190koeg3MICvko5ZbQyjwd4mKtQhCm8xGFUAfAxHuVxvsxyzqOYzZzJSx8e73WOZQKv7VO12sQ4Htz7u+YQnmb23pebDwQ2lJ1odw6doBEZAZwftBlhYfGZtDaUWpdQP9mSQ+Sr02w6YJ+5T8s1kDzKIdP0HspkWGn6TlOGjdA0CLQFdeJUFcrGoA0IE7mt9hD7TWOmlbHPdGq5BvbKT02hVO0AWoI2IywUNIYkNSaFaUzNJylMBFabhFQVSkfocrGCorDeRrbxm/pMexn5jAllD/Sc4mDsF8MaUvo+h4LqHHsZ+cygdJHtiVR+gKxGmSSGNdiwdX6zNSeln6UwEGjFKZVvrgllkshvJouoNQ39pDI7ZXOSw4IJZQ+YUCYJAcltdWM8GsmnE3RHttXafSZQPTChHCLkt1huql/UZtLu91B2htUoe6KRAPt2ho2CBitLv9iZbS+hQcCEsltUo1jiedIYZrmUvvFBniWb+0y9lmugrqPUFUqHpQgliWEN1jT0i3fzU/45SndqgjYg1W9wVdAGhIWS3RaV9YtVBd5QY4Zf7AzagFQXysqgDQgLRfXkZLcFN0xVWGnMoGN3lr2EfMaEMgE7wNJaksXwnUSCtiFsbMi13+cgYE3vXnEBHWt+J4nRVj9POqvzLZDjM7VaroG/4FNbKB1+jpg8pBhTaQPLJptlhdbs9pmUeP5NKIcQeS1k5TVZ8ztZNGXQsTaf3KDtCDl9m4bXZ1JfKFV3Y2NTJo2ROyygkyxW5dtLx2dSxvWW+kLpMO9akhi9zfIpk8WrhUFbEHp2pIJ/EtJHKK35nSRGVZNjIwklh1cKzefrMynz3JtQDjGy28ksbAh2tOgwsDGH1lrLn/SbTUEbECM9hFK1AdgTtBlhYWS1DeIwUJ4rsbQgn6nTcg08fzJGegil472gDQgLEzZZTWggdII+W2zRbp9ZF7QB8aSTUL4PFrFNBmW7yC2w5ne/WZNHa32WDdTrMyaU/UK1DVgftBlhYdr71vzuLwtLLBjmM7u1XFPK1ZY+Qul4N2gDwsKkdeRldJhY7i8RIfpCMXlB2xFyPgjagK6kl1Cq7gB2BW1GGMjqJGPcVmt+7y9Limhty0iz5ya9iAJrgjaiK+l4w1cHbUBYOPBdC+rsLw8NtzLzmfVarinXEy8dhXItNvRaUiiuI6eoltag7UgXVufRui3Xksx9JiXda+knlKrtpKAPI12ZtsbyAfvKIyOCtiD07NZyrQ7aiO5IP6F0pORbJ+yEAu4AABLASURBVB2ZuIH8zHYL6iSiJovIq4UWxPGZVUEb0BPpKZSqu4DtQZsRBjIUmbDRgjqJeGi45fD6TDPOrZaSpKdQOl4P2oCwcOB7ZKOWG9gTNVlEniolP2g7Qs4KLdeUfRmlr1CqbiNFBvVMd4Y1kj2qysb87In7RtKhYsPT+UgLKZ7Nkr5C6Xg1aAPCwmGvk23Dr/0z27OIPFtCQdB2hJyUrk1Cugulag0p1ic0XRnWRPbEjVar7Mo9oyzQ5TMtpEFwNr2F0vEaWIpLMpi5nFzr1riXzTm0vlhsvkmfeSvVa5MQBqFUrQdWBm1GGMhtI3Pa+5aADhAFvX2s+SV9ppY0qE1CGITS8SbQFLQRYeCgd8jPabWeTy8V0WIzLPrOMi3XtGgNhkMoVTuAZUGbEQayOsmY9cbQzhlsFjrvGGMi6TObtVw3B21EXwmHUAKorsNma0wKEzaTX1ozdAM7d4+irTHTBub1kU7g5aCN2B/CI5SOJdgo6Elh7lKyJDr0gmTv59Hy9zJLB/KZ5Vqu9UEbsT+ESyhVa0mzN1WqMqyR7CkfDK1aZbPQecsEsoO2I+TUAG8FbcT+Ei6hBFB9jxTuM5pOzHyL/ILGodMP/I6xRHbbFLR+EgUWpUsAJ57wCaXjRVzqgTEAMqNkHPc8GUMht3JZIc2LLWfSb97Qct0dtBH9IZxC6aLgCzF/5YAZ1kj24a+Fu1ZZm0n7/4y1KLfP7ACWB21EfwmnUAKo7sb8lUlh4kYKJmygOWg7/KADojdPINpsUW4/iQDPa7mm7VgC4RVKMH9lEpnzCvnD6sNXs/z1aFrXWGK53yzWcq0L2oiBEG6hdCzB/JUDJkORYxeFy1/5bDHNlgrkOyu1XDcEbcRACb9Qujl2zF+ZBIY1kT3nFSJB25EM1uXS+vOxFrzxmSpCMhRi+IUSYv7KxWDjLQ6UCZvJn7QuvfvV78mk/fqJZHfaYLx+0gw8m46pQN0xNIQSYl0cXwjajDAw+zUKCuvSc5Shxgw6vjMZ6rMseOMj7cBTWq6hCQAOHaEEUF2Dy7E0BkCGIvOeJyu3Jb1GGWoTOq+ZRLQqx3rf+EgUeEbLtSZoQ5LJ0BJKANXVWNrQgMlrIevEpyFdhmRrh2j5RNo35JETtC0h5wUt19DNZTX0hBJA9R1sWLYBU9BM9kf+kfpi2Qn6w/G0rSqwebl95nUt1/eDNsIPhqZQAqiuxKa8HTAFzWSf+Axkt6VmVkEHRH84ntZXiizC7TNva7m+GbQRfiGavsnyyUHkaODIoM1Id5oKaX/xY0hHTuoMKhERojdPIPLWMKtJ+sxKLddQt9BMKAFEjgPmBG1GutNYRGTJGWSkgli2Cp3XT6RjdYH1uvGZFVqurwRthN+YUMYQORI4Omgz0p2GYiIvnR6sWDZm0HHNJKIWuPGd5VquoUgoT4QJZTwik4GPgj1gA6G+hMhLp5PZmT34uYrV2bRdM4mMndmWAuQzr4fZJ9kVE8quiBQDHwPKgjYlnakrJfLKqUgkb/AEa0UBLTdNILctYwgHKf0nihvkYkgNNmNC2R0iWcB84ICALUlr2nLpfO0UIrUj/I84/6WUpt+MYZjf5xniRICntVyH3CR+JpS9ITIHOBasT3B/UdBVR9G88WB/RCwiRH8xhtbnS2wUIJ9pAP6u5TokR+IyoUyEyATgNLAUk4GwbTItK44jJ5rEPtZbcmi7aQIZ1iXRd7YCz2m5pmX//mRgQtkXRIqAM4ARQZuSzjQWEXllPrQUDixYFgV9spTm346mwEYA8hUF3gTeTOfRyZOBCWVfcX7Lo4DZDOUeTQOkI5PoGyfRunNc/5rKdZm0/2gcnSssidxvWnC1yG1BG5IKmFDuLyIjgJOBUUGbks6snUXzmsPIJ6NvNcIo6ItFtNwxhlyb38Z3KnEiGZph0gaKCWV/EBFgFnAMmH+sv9SMpvWtE8hsy++9DCuzabt9LFgvG99pB17Rcn03aENSDRPKgSAyDDgOmB60KelKRybR1XNp2XQgBV1rlxEh+uAIWh8eTr6aL9JvtuGGSGsI2pBUxIQyGYiMAU7AmuP9pr6EyFsnEG0oJS8KurSQll+PIWd3VvD9xkNOBFeLXB20IamMCWUyETkYl3dpOX39Q18/hnUXnsbo9XkUB23MEGAN8KqWa0vQhqQ6JpTJRiQTOBAXHbd0or6zEXgT1RqpkBxchsEsLMPAD6qBZVquO4I2JF0wofQTkfE4wZyM9e7piY14Atl1g1RIMU4wp2PllwzqcDXItJ9ne7AxoRwM3EAbhwEzsCg5QBOwFngfTdwlTiqkFDe48oGYYPaH3cByYN1QTxzvLyaUg4lIDnAITjQLA7ZmsOnA1R7fB7bRjx+eVEgZTjCnYU3yvlCD61WzMWhD0h0TyiBweZhTcQ/8RMLdj7waJ47rUY0k44BSIcOAQ4GZhLvs+oMCW4BVWq5bgjYmLJhQBo0TzTE4P+ZkYHiwBiWFBvY2rev9OolUfBg4OwwY6dd50oRmXBR7tZZrY9DGhA0TylRDpBCYhBPNCZAWeYS1uJqjW3wUx56QChmBC/ocyNBxa3TiRvZZC2zUco0GbE9oMaFMZVyq0XicYJbiRl0vJNiARhTYyV5h3I6m1vBbUiFjcaJ5AOFrmsfEcT2wScuT484weseEMt1woxiV4IQzJp6l3rpkDRbRiWvKNXn/NwONwA5gJ6qdSTqPr0iFCK631CScL3g06Rk1b8QNVLEVJ47tAdsz5DChDAvO11nkLTm4NKT4JSaiwl6xUNxwWjExdMKo2jZ4hg8eUiG5uNr5eJyAjiA1o+fNuNr6NmCblg++K8PYFxNKY8giFZKBCwKN8pYyXM18sGbhVFzgqwbYFfvfhjdLPUwoDaMLUiF5QHHcko/zdeYBuXH/Z/LPNVLFDVcWiVvagVacKDZ6/zcAjRaASQ9MKA1jgHi+UACs50s4MaE0DMNIQCo6sg3DMFIKE0rDMIwEmFAahmEkwITSMAwjASaUhmEYCRhUoRSRG0TkvsE8Z18RkVUiMj9oO3pDRCaLSKO4PuCGYQwSCYVSRDaKSIv3gG4Xkd+JG+EmbRGRu0Xk5vh1qjpLVRf141g53gtgrYg0eeV1l4hMTYKdG0VkQZyNm1W1UNOkr7VhhIW+1ijPUdVC3OjSxwDXdt1BHINSQxU3MESq8AjwSeBiXPe3OcAbwGlBGmUYRvLYL2FT1W3A33EDpSIii0TkFhF5CdeR/wARGS8ifxGR3SLygYh8ubtjiUi2iDwgIn/yamXHishSEakVkSoR+YW4qRNi+6uIfE1E1gJrReSXIvLjLsf8q4hc5f0907Ov1mtWf9Jb/2/AJcDVXi35r976D2tvIpIpIteIyDoRaRCRN0RkUjfXsAA4HThXVV9T1Q5VrVPVX6rqnd4+PZaHVxN9SER+751nlYgc7W27Fzcm5V89O68WkaleOWR5+0wTkRe87y70yuQ+b1ueiNwnIru8MnhN3PzjRgri/Va/FLQdXUkXd4+IXCIiT/t2AlXtdcHNc7LA+3sSsAq4yfu8CNiMm1Y0CzdKzWLgDlx/2CNwYxee5u1/A3Afru/s34C7gUxv21HAPO84U4HVwFVxdijwDG4E8Hzc/NmVQIa3fSROrMd4dnwAXIMb4OCjuL61M7x97wZu7uU6/x/wNm4yMMHVEkd0Uza3AosTlF+i8mgFPoHrN/wDYFl3Nnmfp3rlkOV9Xgr8t3eNHwHqgfu8bf8O/BU3x3imV77Fie63Lf1fvPvVguvPHVt+0cfvLgK+lCLXsCBJxxoH3AlUec/fe0AFMGyAx93nORiMpa81ysdFpBZY4j3434/bdreqrlLVDmCs98B+R1VbVXU58Fvgs3H7FwNPAeuAy9Xzt6nqG6q6TF2tbCPwf8ApXez4garuVtUWVX0VN/1mrIn7r8AiVd2OE9xC4FZVjajqc8ATwEV9vN4vAdeq6hp1rFDVXd3sNwL3I+gWrxaaqDyWqOqTXjncixPlhIjIZJwb5HrvGpcAf4nbpd2zb7qqdnrla8N1+c856vzIseXrg3nyVHFLichw3Is8HzheVYtwra9S3Cj0aUVfhfI8VS1V1Smq+lVVbYnbFj+B0Xhgt6o2xK3bhBsDMMY84HCciH3Y0VxEDhaRJ0SkWkTqcWLcdR6UrpMl3QNc6v19KU5oYnZsUd1nZJaudvTGJJyQJ2IX7q3ZE30pj+q4v5uBvD7+2GPHjh+SK7587gX+AfxRRCpF5DYRsalyA6JrxkdXN0qXfceJyEoR+bb3+XIRWe25WNaLyL/H7TtfRLaKyHdEpBr4nYi8IyLnxO2TLSI1InKE9/mTnpun1mvyz/TW98XdM1xcQLdSRPaIyOM9XPI3cbXIS72KD6q6RVWvVNWV3rFO8FxCdd7/J8TZvEhEbhKRl7zrflpEYnrwgvd/rWfn8SLyeRFZEvf9M0RkjXfsO0Rkccy1ISLTvc91Xrk8mOj+JSP4Ej+qRiUwXESK4tZNxg1AGuNpXBPz2S4+s//FVc0PUtViXLO562jUXUfwuA84V0Tm4Gbki920SmCS7Btcircj0UggW+jbW28hcKyITOxhe1/Kozd6s7PKO3ZB3LoP/aiq2q6qFap6KHACcDZwWR/PawSEuGyJxbgm+397q3fg7l8xcDnwPyJyZNzXxuJcUlOAfwN+z94KBDjXTpWqLheRg4EHgKtwY3A+iRPGHFX9LM6VFqsV39aNiffi3DmzcCPG/08Pl7IAeLRLZSX+Oofj3G8/w7V8fgL8TURGxO12sXe9o3HupW9760/2/i/17Fza5dgjcUHW73nHXoN7BmLchNOhMtzI9z/v4Ro+JKlRalXdArwM/MALJhwOfBG4v8t+twF/wIll7C1RhPOxNYrIIcBX+nC+rcBruJv3p7ia7iu40bqv9t6m84FzgD9627fj5lPpid8CN4nIQeI4vMsNjJ1/Ic5v+piIHCUiWSJSJCJXiMgX+loevdCjnaq6CXgduEFcMOx47xoBEJFTRWS254SvxzXFLa3Ifx73amqxpdtgZg8civNVlqvqr2MrVfVvqrrOcwMtxj3kJ8V9L+p9p817Bu4DPiEixd72z7K3tXUh8DdVfUZV23E+7nz2FZJuEZFxwJnAFaq6x3sZL+5h917dUsBZwFpVvddztz2AqyidE7fP71T1fe+aHsL5+PvCJ4BVqvqo5xL8Gfu23NpxL5XxnktsSXcHicePdJ6LcM7WSuAx3A18putOqnoTrga40Hu7fBv3BmkAfgMkrA573APMZu8PAXXzR38Sd1NrcMGUy1T1PW+XO4FDvR9yd02Hn+BuzNM4kbkT92Pqjk/j3soP4nym7wBH42qb0Mfy6IEfANd6dn67m+2XAMfjXAA3ezbEpnEYi3ur1uMCY4txD5DhLzE3VWz5zX589xJca+OR+JUicqaILBOXOVGLE4J4t9ROjZvgTVUrgZeA80WkFPccxF7O43Hun9i+UVwLqi9uqUk4d8+ePuzbF7fUpi7rErml+pq/PZ44N5Tn4tsat/1qXGv1Vc8F8YWER+xvFChVFlw1fDNe9HsoLzihrAjajqG60EvEGJdJ8Wjc53nsm8GwCNeK+jPwMHuzQXI9kfg0kO2texwvawOYD2zt5nwXAc8CXwYWxq2/Dngo7rPgxHm+93kDPWRa4IQvimvyJiqLm4GVPT2XuFruq13WvQx8Pq48vhS37fO4wCe42uA+Ue8u2z8HvNzlGrfQTVYBLtjaigt69ng9ad3X2wtOXAn8VnvwhYQZETlGRA4UkQwR+ThwLnv9tEZqsRw4WVxeYgnOf9aVduACYBhwr+djz8GJ5U6gQ0TOBM7ow/kex3UQuRLns4zxEHCWiJzmPT/fwrVCXva29+buqcLlUd8hImWeW+vk7vbFtcqKgXtEZAqAiEwQkZ94LqgngYNF5GLPZXUhzvXwRB+ubSdOsHtyn/0NmC0i53lBqK/hWlh4dlwQF1fYgxPdXt1SaSuUXqSuFveWuz1gc4JiLO7N24jzw3xFVd8K1CIjFjGOLY8BqHO3PIirZb1BD4Kgzm30KVwA4y6cr/0bOIHbg3NP/aW773Y5TgvwJ2Aa8Gjc+jW4QM/PcW6pc3DBm9j84IncPZ/FCfp7uCDTVT2cfzfO79kOvCIiDbgabh3wgbp0u7NxQr0L1xw+W1Vr+nBtzcAtwEuenfO6bK/BvXBu8459KM6fH3NLHePZ1IgryytVdUNv57SpIAwjpIjI9cDBqnppwp1DjFcz3wpcoqrP9+cYaVujNAyjZ7wA6ReBXyfaN4yIyMdEpFREctmbarisv8czoTSMkOGlJG0B/q6qLyTaP6Qcj+s0EnMvnKf7dpTZL6zpbRiGkQCrURqGYSTAhNIwDCMBJpSGYRgJMKE0DMNIgAmlYRhGAv4/IVQIqm2mGMoAAAAASUVORK5CYII=
"
>
</div>

</div>

</div>
</div>

  </div>
<div class="cell border-box-sizing text_cell rendered"><div class="inner_cell">
<div class="text_cell_render border-box-sizing rendered_html">
<h2 id="magsReport">MAGs Report</h2>
</div>
</div>
</div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="o">%</span><span class="k">pylab</span> inline
<span class="kn">from</span> <span class="nn">pandas</span> <span class="k">import</span> <span class="n">Series</span><span class="p">,</span> <span class="n">DataFrame</span><span class="p">,</span> <span class="n">pivot_table</span>
<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
<span class="kn">import</span> <span class="nn">numpy</span>
<span class="kn">from</span> <span class="nn">ipywidgets</span> <span class="k">import</span> <span class="n">interact</span><span class="p">,</span><span class="n">SelectMultiple</span>
<span class="kn">from</span> <span class="nn">IPython.display</span> <span class="k">import</span> <span class="n">display</span>

<span class="n">d</span> <span class="o">=</span> <span class="p">{</span> <span class="s1">&#39;Class&#39;</span>   <span class="p">:</span> <span class="n">Series</span><span class="p">(</span> <span class="p">[</span><span class="s1">&#39;a&#39;</span><span class="p">,</span>  <span class="s1">&#39;b&#39;</span><span class="p">,</span> <span class="s1">&#39;b&#39;</span><span class="p">,</span><span class="s1">&#39;a&#39;</span><span class="p">,</span><span class="s1">&#39;a&#39;</span><span class="p">,</span>  <span class="s1">&#39;b&#39;</span><span class="p">,</span> <span class="s1">&#39;b&#39;</span><span class="p">,</span><span class="s1">&#39;a&#39;</span><span class="p">,</span><span class="s1">&#39;a&#39;</span><span class="p">,</span>  <span class="s1">&#39;b&#39;</span><span class="p">,</span> <span class="s1">&#39;b&#39;</span><span class="p">,</span><span class="s1">&#39;a&#39;</span><span class="p">,</span><span class="s1">&#39;a&#39;</span><span class="p">,</span><span class="s1">&#39;b&#39;</span><span class="p">,</span><span class="s1">&#39;b&#39;</span><span class="p">,</span><span class="s1">&#39;b&#39;</span><span class="p">]),</span>
  <span class="s1">&#39;Area&#39;</span>   <span class="p">:</span> <span class="n">Series</span><span class="p">(</span> <span class="p">[</span><span class="s1">&#39;North&#39;</span><span class="p">,</span><span class="s1">&#39;East&#39;</span><span class="p">,</span> <span class="s1">&#39;South&#39;</span><span class="p">,</span> <span class="s1">&#39;West&#39;</span><span class="p">,</span><span class="s1">&#39;North&#39;</span><span class="p">,</span><span class="s1">&#39;East&#39;</span><span class="p">,</span> <span class="s1">&#39;South&#39;</span><span class="p">,</span> <span class="s1">&#39;West&#39;</span><span class="p">,</span><span class="s1">&#39;North&#39;</span><span class="p">,</span><span class="s1">&#39;East&#39;</span><span class="p">,</span> <span class="s1">&#39;South&#39;</span><span class="p">,</span> <span class="s1">&#39;West&#39;</span><span class="p">,</span><span class="s1">&#39;South&#39;</span><span class="p">,</span> <span class="s1">&#39;West&#39;</span><span class="p">,</span><span class="s1">&#39;South&#39;</span><span class="p">,</span> <span class="s1">&#39;West&#39;</span><span class="p">]),</span>
  <span class="s1">&#39;Type&#39;</span> <span class="p">:</span> <span class="n">Series</span><span class="p">(</span> <span class="p">[</span><span class="s1">&#39;square&#39;</span><span class="p">,</span> <span class="s1">&#39;round&#39;</span><span class="p">,</span><span class="s1">&#39;square&#39;</span><span class="p">,</span> <span class="s1">&#39;round&#39;</span><span class="p">,</span> <span class="s1">&#39;round&#39;</span><span class="p">,</span> <span class="s1">&#39;square&#39;</span><span class="p">,</span> <span class="s1">&#39;round&#39;</span><span class="p">,</span> <span class="s1">&#39;square&#39;</span><span class="p">,</span> <span class="s1">&#39;round&#39;</span><span class="p">,</span> <span class="s1">&#39;square&#39;</span><span class="p">,</span><span class="s1">&#39;round&#39;</span><span class="p">,</span> <span class="s1">&#39;square&#39;</span><span class="p">,]),</span>
  <span class="s1">&#39;Web&#39;</span>  <span class="p">:</span> <span class="n">Series</span><span class="p">(</span> <span class="p">[</span><span class="s1">&#39;Y&#39;</span><span class="p">,</span><span class="s1">&#39;N&#39;</span><span class="p">,</span><span class="s1">&#39;N&#39;</span><span class="p">,</span><span class="s1">&#39;Y&#39;</span><span class="p">,</span><span class="s1">&#39;Y&#39;</span><span class="p">,</span><span class="s1">&#39;N&#39;</span><span class="p">,</span><span class="s1">&#39;N&#39;</span><span class="p">,</span><span class="s1">&#39;Y&#39;</span><span class="p">,</span><span class="s1">&#39;Y&#39;</span><span class="p">,</span><span class="s1">&#39;N&#39;</span><span class="p">,</span><span class="s1">&#39;N&#39;</span><span class="p">,</span><span class="s1">&#39;Y&#39;</span><span class="p">,</span><span class="s1">&#39;Y&#39;</span><span class="p">,</span><span class="s1">&#39;N&#39;</span><span class="p">,</span><span class="s1">&#39;N&#39;</span><span class="p">,</span><span class="s1">&#39;Y&#39;</span><span class="p">]),</span>
  <span class="s1">&#39;Agent&#39;</span>   <span class="p">:</span> <span class="n">Series</span><span class="p">(</span> <span class="p">[</span><span class="s1">&#39;Mike&#39;</span><span class="p">,</span>  <span class="s1">&#39;John&#39;</span><span class="p">,</span> <span class="s1">&#39;Pete&#39;</span><span class="p">,</span><span class="s1">&#39;Mike&#39;</span><span class="p">,</span>  <span class="s1">&#39;John&#39;</span><span class="p">,</span> <span class="s1">&#39;Pete&#39;</span><span class="p">,</span><span class="s1">&#39;Mike&#39;</span><span class="p">,</span>  <span class="s1">&#39;John&#39;</span><span class="p">,</span> <span class="s1">&#39;Pete&#39;</span><span class="p">,</span><span class="s1">&#39;Mike&#39;</span><span class="p">,</span>  <span class="s1">&#39;John&#39;</span><span class="p">,</span> <span class="s1">&#39;Pete&#39;</span><span class="p">,</span><span class="s1">&#39;John&#39;</span><span class="p">,</span> <span class="s1">&#39;Pete&#39;</span><span class="p">,</span><span class="s1">&#39;John&#39;</span><span class="p">,</span> <span class="s1">&#39;Pete&#39;</span><span class="p">]),</span>
  <span class="s1">&#39;Income&#39;</span>   <span class="p">:</span> <span class="n">Series</span><span class="p">(</span> <span class="p">[</span><span class="mf">20.</span><span class="p">,</span> <span class="mf">40.</span><span class="p">,</span> <span class="mf">90.</span><span class="p">,</span> <span class="mf">20.</span><span class="p">]),</span>
  <span class="s1">&#39;Profit&#39;</span> <span class="p">:</span> <span class="n">Series</span><span class="p">(</span> <span class="p">[</span><span class="mf">1.</span><span class="p">,</span> <span class="mf">2.</span><span class="p">,</span> <span class="mf">3.</span><span class="p">,</span> <span class="mf">4.</span><span class="p">,</span><span class="mf">1.</span><span class="p">,</span> <span class="mf">2.</span><span class="p">,</span> <span class="mf">3.</span><span class="p">,</span> <span class="mf">4.</span><span class="p">,</span><span class="mf">1.</span><span class="p">,</span> <span class="mf">2.</span><span class="p">,</span> <span class="mf">3.</span><span class="p">,</span> <span class="mf">4.</span><span class="p">,</span><span class="mf">1.</span><span class="p">,</span> <span class="mf">2.</span><span class="p">,</span> <span class="mf">3.</span><span class="p">,</span> <span class="mf">4.</span><span class="p">]),</span>
  <span class="s1">&#39;Stock&#39;</span> <span class="p">:</span> <span class="n">Series</span><span class="p">(</span> <span class="p">[</span><span class="mf">20.</span><span class="p">,</span> <span class="mf">23.</span><span class="p">,</span> <span class="mf">33.</span><span class="p">,</span> <span class="mf">43.</span><span class="p">,</span><span class="mf">12.</span><span class="p">,</span> <span class="mf">21.</span><span class="p">,</span> <span class="mf">310.</span><span class="p">,</span> <span class="mf">41.</span><span class="p">,</span><span class="mf">11.</span><span class="p">,</span> <span class="mf">21.</span><span class="p">,</span> <span class="mf">31.</span><span class="p">,</span> <span class="mf">41.</span><span class="p">,</span><span class="mf">11.</span><span class="p">,</span> <span class="mf">22.</span><span class="p">,</span> <span class="mf">34.</span><span class="p">,</span> <span class="mf">54.</span><span class="p">]</span> <span class="p">)</span>
 <span class="p">}</span>
<span class="n">df</span> <span class="o">=</span> <span class="n">DataFrame</span><span class="p">(</span><span class="n">d</span><span class="p">)</span>


<span class="k">def</span> <span class="nf">my_pivot</span><span class="p">(</span> <span class="n">rows</span><span class="p">,</span> <span class="n">values</span><span class="p">,</span> <span class="n">aggfunc</span><span class="p">):</span>
    <span class="n">dfp</span> <span class="o">=</span> <span class="n">df</span>
    <span class="n">piv</span> <span class="o">=</span> <span class="n">pivot_table</span><span class="p">(</span> <span class="n">dfp</span><span class="p">,</span> <span class="n">rows</span><span class="o">=</span><span class="n">rows</span><span class="p">,</span> <span class="n">values</span><span class="o">=</span><span class="n">values</span><span class="p">,</span> <span class="n">aggfunc</span><span class="o">=</span><span class="n">aggfunc</span><span class="p">)</span>


<span class="n">i</span> <span class="o">=</span> <span class="n">interact</span><span class="p">(</span> <span class="n">my_pivot</span><span class="p">,</span>
             <span class="n">rows</span>    <span class="o">=</span> <span class="n">SelectMultiple</span><span class="p">(</span><span class="n">options</span><span class="o">=</span><span class="nb">list</span><span class="p">(</span><span class="n">df</span><span class="o">.</span><span class="n">columns</span><span class="p">)),</span> 
             <span class="n">values</span>  <span class="o">=</span> <span class="n">SelectMultiple</span><span class="p">(</span><span class="n">options</span><span class="o">=</span><span class="p">[</span><span class="s1">&#39;Profit&#39;</span><span class="p">,</span> <span class="s1">&#39;Stock&#39;</span><span class="p">]),</span>
             <span class="n">aggfunc</span> <span class="o">=</span> <span class="n">SelectMultiple</span><span class="p">(</span><span class="n">options</span><span class="o">=</span><span class="p">{</span> <span class="s1">&#39;sum&#39;</span> <span class="p">:</span> <span class="n">numpy</span><span class="o">.</span><span class="n">sum</span><span class="p">,</span> <span class="s1">&#39;ave&#39;</span> <span class="p">:</span> <span class="n">numpy</span><span class="o">.</span><span class="n">average</span> <span class="p">}))</span>
<span class="n">i</span>

<span class="kn">import</span> <span class="nn">chart_studio.plotly</span> <span class="k">as</span> <span class="nn">py</span>
<span class="kn">import</span> <span class="nn">plotly.graph_objects</span> <span class="k">as</span> <span class="nn">go</span>
<span class="kn">from</span> <span class="nn">ipywidgets</span> <span class="k">import</span> <span class="n">Text</span><span class="p">,</span> <span class="n">Dropdown</span><span class="p">,</span> <span class="n">Output</span><span class="p">,</span> <span class="n">AppLayout</span><span class="p">,</span> <span class="n">interact</span>
<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
<span class="c1"># py.offline.init_notebook_mode(connected=True)</span>

<span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span> 
<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span> 
  
<span class="o">%</span> <span class="n">matplotlib</span> <span class="n">inline</span> 
<span class="kn">from</span> <span class="nn">plotly</span> <span class="k">import</span> <span class="n">__version__</span> 
<span class="kn">import</span> <span class="nn">cufflinks</span> <span class="k">as</span> <span class="nn">cf</span> 
  
<span class="kn">from</span> <span class="nn">plotly.offline</span> <span class="k">import</span> <span class="n">download_plotlyjs</span><span class="p">,</span> <span class="n">init_notebook_mode</span><span class="p">,</span> <span class="n">plot</span><span class="p">,</span> <span class="n">iplot</span> 
  
<span class="c1"># to get the connection </span>
<span class="n">init_notebook_mode</span><span class="p">(</span><span class="n">connected</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span> 
  
<span class="c1"># plotly also serves online, </span>
<span class="c1"># but we are using just a sample </span>
<span class="n">cf</span><span class="o">.</span><span class="n">go_offline</span> 
  
<span class="c1"># creating dataframes </span>
<span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">randn</span><span class="p">(</span><span class="mi">100</span><span class="p">,</span> <span class="mi">4</span><span class="p">),</span> <span class="n">columns</span> <span class="o">=</span><span class="s1">&#39;A B C D&#39;</span><span class="o">.</span><span class="n">split</span><span class="p">())</span> 
  
<span class="n">df2</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">({</span><span class="s1">&#39;Category&#39;</span><span class="p">:[</span><span class="s1">&#39;A&#39;</span><span class="p">,</span> <span class="s1">&#39;B&#39;</span><span class="p">,</span> <span class="s1">&#39;C&#39;</span><span class="p">],</span> <span class="s1">&#39;Values&#39;</span><span class="p">:[</span><span class="mi">32</span><span class="p">,</span> <span class="mi">43</span><span class="p">,</span> <span class="mi">50</span><span class="p">]})</span> 
<span class="n">df2</span><span class="o">.</span><span class="n">head</span><span class="p">()</span> 

<span class="kn">import</span> <span class="nn">plotly.graph_objects</span> <span class="k">as</span> <span class="nn">go</span>
<span class="kn">import</span> <span class="nn">plotly.io</span> <span class="k">as</span> <span class="nn">pio</span>

<span class="n">fig</span> <span class="o">=</span> <span class="n">go</span><span class="o">.</span><span class="n">Figure</span><span class="p">(</span><span class="n">go</span><span class="o">.</span><span class="n">Scatter</span><span class="p">(</span><span class="n">x</span><span class="o">=</span><span class="p">[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="mi">4</span><span class="p">],</span> <span class="n">y</span><span class="o">=</span><span class="p">[</span><span class="mi">4</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">1</span><span class="p">]))</span>
<span class="n">fig</span><span class="o">.</span><span class="n">update_layout</span><span class="p">(</span><span class="n">title_text</span><span class="o">=</span><span class="s1">&#39;hello world&#39;</span><span class="p">)</span>
<span class="n">pio</span><span class="o">.</span><span class="n">show</span><span class="p">(</span><span class="n">fig</span><span class="p">)</span>

<span class="kn">import</span> <span class="nn">chart_studio.plotly</span> <span class="k">as</span> <span class="nn">py</span>
<span class="kn">import</span> <span class="nn">plotly.graph_objects</span> <span class="k">as</span> <span class="nn">go</span>
<span class="kn">import</span> <span class="nn">plotly.io</span> <span class="k">as</span> <span class="nn">pio</span>

<span class="c1"># these two lines allow your code to show up in a notebook</span>
<span class="kn">from</span> <span class="nn">plotly.offline</span> <span class="k">import</span> <span class="n">init_notebook_mode</span><span class="p">,</span> <span class="n">iplot</span>
<span class="n">init_notebook_mode</span><span class="p">()</span>


<span class="n">trace0</span> <span class="o">=</span> <span class="n">go</span><span class="o">.</span><span class="n">Scatter</span><span class="p">(</span>
    <span class="n">x</span><span class="o">=</span><span class="p">[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="mi">4</span><span class="p">],</span>
    <span class="n">y</span><span class="o">=</span><span class="p">[</span><span class="mi">10</span><span class="p">,</span> <span class="mi">15</span><span class="p">,</span> <span class="mi">13</span><span class="p">,</span> <span class="mi">17</span><span class="p">]</span>
<span class="p">)</span>
<span class="n">trace1</span> <span class="o">=</span> <span class="n">go</span><span class="o">.</span><span class="n">Scatter</span><span class="p">(</span>
    <span class="n">x</span><span class="o">=</span><span class="p">[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="mi">4</span><span class="p">],</span>
    <span class="n">y</span><span class="o">=</span><span class="p">[</span><span class="mi">16</span><span class="p">,</span> <span class="mi">5</span><span class="p">,</span> <span class="mi">11</span><span class="p">,</span> <span class="mi">9</span><span class="p">]</span>
<span class="p">)</span>
<span class="n">data</span> <span class="o">=</span> <span class="p">[</span><span class="n">trace0</span><span class="p">,</span> <span class="n">trace1</span><span class="p">]</span>

<span class="n">py</span><span class="o">.</span><span class="n">offline</span><span class="o">.</span><span class="n">iplot</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">filename</span> <span class="o">=</span> <span class="s1">&#39;basic-line&#39;</span><span class="p">)</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="k">as</span> <span class="nn">plt</span>
<span class="kn">from</span> <span class="nn">matplotlib_venn</span> <span class="k">import</span> <span class="n">venn2</span>
 
<span class="c1"># First way to call the 2 group Venn diagram:</span>
<span class="c1"># venn2(subsets = (10, 5, 2), set_labels = (&#39;Group A&#39;, &#39;Group B&#39;))</span>
<span class="c1"># plt.show()</span>
 
<span class="c1"># Second way</span>
<span class="n">venn2</span><span class="p">([</span><span class="nb">set</span><span class="p">([</span><span class="s1">&#39;A&#39;</span><span class="p">,</span> <span class="s1">&#39;B&#39;</span><span class="p">,</span> <span class="s1">&#39;C&#39;</span><span class="p">,</span> <span class="s1">&#39;D&#39;</span><span class="p">]),</span> <span class="nb">set</span><span class="p">([</span><span class="s1">&#39;D&#39;</span><span class="p">,</span> <span class="s1">&#39;E&#39;</span><span class="p">,</span> <span class="s1">&#39;F&#39;</span><span class="p">])])</span>
<span class="n">plt</span><span class="o">.</span><span class="n">show</span><span class="p">()</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="o">/</span><span class="n">mnt</span><span class="o">/</span><span class="n">research</span><span class="o">/</span><span class="n">ShadeLab</span><span class="o">/</span><span class="n">GLBRC</span><span class="o">/</span><span class="n">annotations</span><span class="o">/</span><span class="n">EukAnnotationFilteredGenes</span><span class="o">.</span><span class="n">txt</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span>%%bash
mv Final.Contigs.Filtered.bed /mnt/gs18/scratch/users/dooleys1/bowtieDB/Final.contigs.filtered.bed
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">singleFrame</span> <span class="o">=</span> <span class="n">read_csv</span><span class="p">(</span><span class="s2">&quot;mapping/metaG/fullAssembly/counts/G5R1_NF_03OCT2016_LD1.krona.kegg.minpath.tab&quot;</span><span class="p">,</span><span class="n">sep</span><span class="o">=</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>

<span class="kn">from</span> <span class="nn">numpy</span> <span class="k">import</span> <span class="n">zeros</span>
<span class="n">cols</span> <span class="o">=</span> <span class="p">[</span><span class="s2">&quot;Level1&quot;</span><span class="p">,</span><span class="s2">&quot;Level2&quot;</span><span class="p">,</span><span class="s2">&quot;Level3&quot;</span><span class="p">]</span>
<span class="n">cols</span> <span class="o">+=</span> <span class="nb">list</span><span class="p">(</span><span class="n">metadataG</span><span class="o">.</span><span class="n">index</span><span class="p">)</span>
<span class="n">allSampleCounts</span> <span class="o">=</span> <span class="n">DataFrame</span><span class="p">(</span><span class="n">zeros</span><span class="p">((</span><span class="mi">157</span><span class="p">,</span><span class="mi">139</span><span class="p">)),</span><span class="n">index</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span><span class="n">columns</span><span class="o">=</span><span class="n">cols</span><span class="p">)</span>
<span class="n">allSampleCounts</span><span class="p">[[</span><span class="s2">&quot;Level1&quot;</span><span class="p">,</span><span class="s2">&quot;Level2&quot;</span><span class="p">,</span><span class="s2">&quot;Level3&quot;</span><span class="p">]]</span> <span class="o">=</span> <span class="n">singleFrame</span><span class="p">[[</span><span class="s2">&quot;Level1&quot;</span><span class="p">,</span><span class="s2">&quot;Level2&quot;</span><span class="p">,</span><span class="s2">&quot;Level3&quot;</span><span class="p">]]</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">singleFrame</span><span class="o">.</span><span class="n">head</span><span class="p">()</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="kn">from</span> <span class="nn">glob</span> <span class="k">import</span> <span class="n">glob</span>

<span class="n">path</span> <span class="o">=</span> <span class="s1">&#39;mapping/metaG/fullAssembly/counts&#39;</span> 
<span class="n">all_files</span> <span class="o">=</span> <span class="n">glob</span><span class="p">(</span><span class="n">path</span> <span class="o">+</span> <span class="s2">&quot;/*.tab&quot;</span><span class="p">)</span>

<span class="k">for</span> <span class="n">filename</span> <span class="ow">in</span> <span class="n">all_files</span><span class="p">:</span>
    <span class="n">sampleID</span> <span class="o">=</span> <span class="n">filename</span><span class="p">[</span><span class="n">filename</span><span class="o">.</span><span class="n">rfind</span><span class="p">(</span><span class="s1">&#39;/&#39;</span><span class="p">)</span><span class="o">+</span><span class="mi">1</span><span class="p">:</span><span class="n">filename</span><span class="o">.</span><span class="n">rfind</span><span class="p">(</span><span class="s1">&#39;.krona&#39;</span><span class="p">)]</span>
    <span class="n">df</span> <span class="o">=</span> <span class="n">read_csv</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="n">index_col</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">header</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span><span class="n">sep</span><span class="o">=</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
    <span class="n">allSampleCounts</span><span class="p">[</span><span class="n">sampleID</span><span class="p">]</span> <span class="o">=</span> <span class="n">df</span><span class="p">[</span><span class="n">sampleID</span><span class="p">]</span>

<span class="n">allSampleCounts</span><span class="o">.</span><span class="n">head</span><span class="p">()</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="nb">len</span><span class="p">(</span><span class="n">allSampleCounts</span><span class="o">.</span><span class="n">Level3</span><span class="o">.</span><span class="n">unique</span><span class="p">())</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="c1"># Interact with specification of arguments</span>
<span class="c1"># @interact</span>
<span class="c1"># def show_articles_more_than(column=[&#39;total_reads&#39;, &#39;paired_total&#39;, &#39;paired_aligned_none&#39;, &#39;paired_aligned_one&#39;], </span>
<span class="c1">#                             x=(0, 20000000, 50000)):</span>
<span class="c1">#     return metadataG.loc[metadataG[column] &gt; x]</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">metadataT</span> <span class="o">=</span> <span class="n">read_csv</span><span class="p">(</span><span class="s2">&quot;metadata/GLBRC_MetaT_Metadata.tsv&quot;</span><span class="p">,</span><span class="n">sep</span><span class="o">=</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
<span class="n">metadataT</span><span class="o">.</span><span class="n">set_index</span><span class="p">(</span><span class="s2">&quot;nucleic_acid_name&quot;</span><span class="p">,</span><span class="n">inplace</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>

<span class="c1">#for metaT</span>
<span class="n">metadataT</span><span class="o">.</span><span class="n">drop</span><span class="p">([</span><span class="s2">&quot;name&quot;</span><span class="p">,</span> <span class="s2">&quot;day&quot;</span><span class="p">,</span> <span class="s2">&quot;year&quot;</span><span class="p">,</span> <span class="s2">&quot;time&quot;</span><span class="p">,</span> <span class="s2">&quot;weather&quot;</span><span class="p">,</span> <span class="s2">&quot;air_temp_c&quot;</span><span class="p">,</span> <span class="s2">&quot;notes&quot;</span><span class="p">,</span> <span class="s2">&quot;rep&quot;</span><span class="p">,</span> <span class="s2">&quot;pseudorep&quot;</span><span class="p">,</span> <span class="s2">&quot;MMPRNT_ID&quot;</span><span class="p">,</span> <span class="s2">&quot;time_zone&quot;</span><span class="p">,</span> <span class="s2">&quot;longitude&quot;</span><span class="p">,</span> \
               <span class="s2">&quot;latitude&quot;</span><span class="p">,</span> <span class="s2">&quot;altitude&quot;</span><span class="p">,</span> <span class="s2">&quot;location&quot;</span><span class="p">,</span> <span class="s2">&quot;country&quot;</span><span class="p">,</span> <span class="s2">&quot;soil_name&quot;</span><span class="p">,</span> <span class="s2">&quot;number_cores&quot;</span><span class="p">,</span> <span class="s2">&quot;SPNL_date&quot;</span><span class="p">,</span> <span class="s2">&quot;pH&quot;</span><span class="p">,</span> <span class="s2">&quot;lime_index&quot;</span><span class="p">,</span> <span class="s2">&quot;P_ppm&quot;</span><span class="p">,</span> <span class="s2">&quot;K_ppm&quot;</span><span class="p">,</span> \
               <span class="s2">&quot;Ca_ppm&quot;</span><span class="p">,</span> <span class="s2">&quot;Mg_ppm&quot;</span><span class="p">,</span> <span class="s2">&quot;organic_matter&quot;</span><span class="p">,</span> <span class="s2">&quot;NO3N_ppm&quot;</span><span class="p">,</span> <span class="s2">&quot;NH4_ppm&quot;</span><span class="p">,</span> <span class="s2">&quot;soil_moisture_percent&quot;</span><span class="p">,</span> <span class="s2">&quot;soil_temp_10cm&quot;</span><span class="p">,</span> <span class="s2">&quot;LDMC_mg_per_g&quot;</span><span class="p">,</span> \
               <span class="s2">&quot;nitrogen_percent&quot;</span><span class="p">,</span> <span class="s2">&quot;carbon_percent&quot;</span><span class="p">,</span> <span class="s2">&quot;carbon_per_nitrogen&quot;</span><span class="p">,</span> <span class="s2">&quot;height_mean_cm&quot;</span><span class="p">,</span> <span class="s2">&quot;mass_per_leaf_g&quot;</span><span class="p">,</span> <span class="s2">&quot;date_of_extraction&quot;</span><span class="p">,</span>\
               <span class="s2">&quot;nucleic_acid_type&quot;</span><span class="p">,</span> <span class="s2">&quot;replicate_extraction&quot;</span><span class="p">,</span> <span class="s2">&quot;source&quot;</span><span class="p">,</span> <span class="s2">&quot;source_mass&quot;</span><span class="p">,</span> <span class="s2">&quot;extraction_method&quot;</span><span class="p">,</span> <span class="s2">&quot;elution_vol_ul&quot;</span><span class="p">,</span> <span class="s2">&quot;concentration_ng_per_ul&quot;</span><span class="p">,</span>\
               <span class="s2">&quot;ratio_260_280&quot;</span><span class="p">,</span> <span class="s2">&quot;conc_ng_per_g_source&quot;</span><span class="p">,</span> <span class="s2">&quot;extracted_by&quot;</span><span class="p">,</span> <span class="s2">&quot;sequence_name&quot;</span><span class="p">,</span> <span class="s2">&quot;sequencing_date&quot;</span><span class="p">,</span> <span class="s2">&quot;conc_sent_ng_per_ul&quot;</span><span class="p">,</span> \
               <span class="s2">&quot;sequencing_type&quot;</span><span class="p">,</span> <span class="s2">&quot;sequencing_facility&quot;</span><span class="p">,</span> <span class="s2">&quot;primers&quot;</span><span class="p">,</span> <span class="s2">&quot;submitted_for_sequencing&quot;</span><span class="p">,</span> <span class="s2">&quot;sequencing_successful&quot;</span><span class="p">,</span> <span class="s2">&quot;duplicate_submitted&quot;</span><span class="p">,</span>\
               <span class="s2">&quot;dup_sequencing_name&quot;</span><span class="p">,</span> <span class="s2">&quot;exclude_from_analysis&quot;</span><span class="p">,</span> <span class="s2">&quot;itemID_JGI&quot;</span><span class="p">,</span> <span class="s2">&quot;sampleID_JGI&quot;</span><span class="p">,</span> <span class="s2">&quot;barcode&quot;</span><span class="p">,</span> <span class="s2">&quot;JGI_library&quot;</span><span class="p">,</span> <span class="s2">&quot;HPCC_path&quot;</span><span class="p">,</span> <span class="s2">&quot;JGI_taxonOID&quot;</span><span class="p">,</span>\
               <span class="s2">&quot;JGI_rawdataname&quot;</span><span class="p">,</span> <span class="s2">&quot;time_numeric&quot;</span><span class="p">,</span> <span class="s2">&quot;date&quot;</span><span class="p">,</span> <span class="s2">&quot;precipitation&quot;</span><span class="p">,</span> <span class="s2">&quot;Air_temp_mean&quot;</span><span class="p">,</span> <span class="s2">&quot;air_temp_max&quot;</span><span class="p">,</span> <span class="s2">&quot;Air_Temp_Min&quot;</span><span class="p">,</span>\
               <span class="s2">&quot;Air_Pressure&quot;</span><span class="p">,</span> <span class="s2">&quot;RH&quot;</span><span class="p">,</span> <span class="s2">&quot;AH&quot;</span><span class="p">,</span> <span class="s2">&quot;Wind_Speed_Mean&quot;</span><span class="p">,</span> <span class="s2">&quot;Wind_Direction_Mean&quot;</span><span class="p">,</span> <span class="s2">&quot;Solar_Radiation&quot;</span><span class="p">,</span> <span class="s2">&quot;PAR&quot;</span><span class="p">,</span> <span class="s2">&quot;soil_temp_5_cm_bare_avg&quot;</span><span class="p">,</span> \
               <span class="s2">&quot;soil_temp_5_cm_sod_avg&quot;</span><span class="p">],</span><span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span><span class="n">inplace</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span> 

<span class="k">for</span> <span class="nb">id</span> <span class="ow">in</span> <span class="n">metadataT</span><span class="o">.</span><span class="n">index</span><span class="p">:</span> <span class="n">metadataT</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="nb">id</span><span class="p">,</span><span class="s2">&quot;type&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="n">metadataT</span><span class="p">[</span><span class="n">metadataT</span><span class="o">.</span><span class="n">index</span> <span class="o">==</span> <span class="nb">id</span><span class="p">]</span><span class="o">.</span><span class="n">plot_name</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">0</span><span class="p">:</span><span class="mi">2</span><span class="p">]</span>
<span class="n">metadataT</span><span class="p">[</span><span class="s1">&#39;Date&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">to_datetime</span><span class="p">(</span><span class="n">metadataT</span><span class="o">.</span><span class="n">sampling_date</span><span class="p">)</span>
<span class="n">metadataT</span><span class="o">=</span><span class="n">metadataT</span><span class="o">.</span><span class="n">sort_values</span><span class="p">(</span><span class="n">by</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;type&quot;</span><span class="p">,</span><span class="s2">&quot;Date&quot;</span><span class="p">,</span><span class="s2">&quot;treatment&quot;</span><span class="p">,</span><span class="s2">&quot;plot_name&quot;</span><span class="p">])</span>
<span class="n">metadataT</span><span class="o">.</span><span class="n">head</span><span class="p">()</span>

<span class="c1">#Reads After host removal</span>
<span class="n">metaT_Reads</span> <span class="o">=</span> <span class="n">read_csv</span><span class="p">(</span><span class="s2">&quot;mapping/metaT/fullAssembly/multiqc_data/multiqc_bowtie2.txt&quot;</span><span class="p">,</span><span class="n">sep</span><span class="o">=</span><span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">)</span>
<span class="k">for</span> <span class="nb">id</span> <span class="ow">in</span> <span class="n">metaT_Reads</span><span class="o">.</span><span class="n">index</span><span class="p">:</span> <span class="n">metaT_Reads</span><span class="o">.</span><span class="n">at</span><span class="p">[</span><span class="nb">id</span><span class="p">,</span><span class="s2">&quot;Sample&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="n">metaT_Reads</span><span class="o">.</span><span class="n">at</span><span class="p">[</span><span class="nb">id</span><span class="p">,</span><span class="s2">&quot;Sample&quot;</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;.stat&quot;</span><span class="p">,</span><span class="s2">&quot;&quot;</span><span class="p">)</span>
<span class="n">metaT_Reads</span><span class="o">.</span><span class="n">set_index</span><span class="p">(</span><span class="s2">&quot;Sample&quot;</span><span class="p">,</span><span class="n">inplace</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>

<span class="n">metadataT</span> <span class="o">=</span> <span class="n">merge</span><span class="p">(</span><span class="n">metadataT</span><span class="p">,</span><span class="n">metaT_Reads</span><span class="p">,</span><span class="n">left_index</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span><span class="n">right_index</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="n">metadataT</span><span class="o">.</span><span class="n">sort_values</span><span class="p">(</span><span class="s2">&quot;Date&quot;</span><span class="p">,</span><span class="n">inplace</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">fig</span><span class="p">,</span> <span class="n">ax</span> <span class="o">=</span> <span class="n">plt</span><span class="o">.</span><span class="n">subplots</span><span class="p">(</span><span class="n">figsize</span><span class="o">=</span><span class="p">(</span><span class="mi">15</span><span class="p">,</span><span class="mi">7</span><span class="p">))</span>
<span class="c1"># G5Data = metadataG[metadataG[&#39;type&#39;] == &#39;G5&#39;]</span>
<span class="c1"># G5Data.groupby([&#39;Date&#39;,&#39;plot_name&#39;]).sum()[[&#39;aligned&#39;,&#39;total_reads&#39;]].unstack().plot(ax=ax);</span>
<span class="n">ax</span> <span class="o">=</span> <span class="n">metadataG</span><span class="o">.</span><span class="n">groupby</span><span class="p">([</span><span class="s1">&#39;Date&#39;</span><span class="p">,</span><span class="s1">&#39;plot_name&#39;</span><span class="p">])</span><span class="o">.</span><span class="n">sum</span><span class="p">()[</span><span class="s1">&#39;pLantAligned&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">unstack</span><span class="p">()</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">ax</span><span class="o">=</span><span class="n">ax</span><span class="p">,</span><span class="n">title</span><span class="o">=</span><span class="s2">&quot;% Reads Aligning to Respective Plant Host Assembly G5=Switchgrass G6=Miscanthus&quot;</span><span class="p">);</span> <span class="c1">#legend=false</span>
<span class="n">patches</span><span class="p">,</span> <span class="n">labels</span> <span class="o">=</span> <span class="n">ax</span><span class="o">.</span><span class="n">get_legend_handles_labels</span><span class="p">()</span>
<span class="n">ax</span><span class="o">.</span><span class="n">set_ylabel</span><span class="p">(</span><span class="s2">&quot;% Reads&quot;</span><span class="p">,</span><span class="n">fontsize</span><span class="o">=</span><span class="mi">14</span><span class="p">)</span>
<span class="n">ax</span><span class="o">.</span><span class="n">set_ylim</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="mi">100</span><span class="p">)</span>
<span class="c1"># ax.legend(patches, labels, loc=&#39;best&#39;)</span>
<span class="c1"># Shrink current axis by 20%</span>
<span class="n">box</span> <span class="o">=</span> <span class="n">ax</span><span class="o">.</span><span class="n">get_position</span><span class="p">()</span>
<span class="n">ax</span><span class="o">.</span><span class="n">set_position</span><span class="p">([</span><span class="n">box</span><span class="o">.</span><span class="n">x0</span><span class="p">,</span> <span class="n">box</span><span class="o">.</span><span class="n">y0</span><span class="p">,</span> <span class="n">box</span><span class="o">.</span><span class="n">width</span> <span class="o">*</span> <span class="mf">0.8</span><span class="p">,</span> <span class="n">box</span><span class="o">.</span><span class="n">height</span><span class="p">])</span>

<span class="c1"># Put a legend to the right of the current axis</span>
<span class="n">ax</span><span class="o">.</span><span class="n">legend</span><span class="p">(</span><span class="n">loc</span><span class="o">=</span><span class="s1">&#39;center left&#39;</span><span class="p">,</span> <span class="n">bbox_to_anchor</span><span class="o">=</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mf">0.5</span><span class="p">))</span>

<span class="n">fig</span> <span class="o">=</span> <span class="n">ax</span><span class="o">.</span><span class="n">get_figure</span><span class="p">()</span>
<span class="n">fig</span><span class="o">.</span><span class="n">savefig</span><span class="p">(</span><span class="s1">&#39;images/PlantAlignedReads.png&#39;</span><span class="p">)</span>

<span class="n">fig</span><span class="p">,</span> <span class="n">ax</span> <span class="o">=</span> <span class="n">plt</span><span class="o">.</span><span class="n">subplots</span><span class="p">(</span><span class="n">figsize</span><span class="o">=</span><span class="p">(</span><span class="mi">15</span><span class="p">,</span><span class="mi">7</span><span class="p">))</span>
<span class="n">G6Data</span> <span class="o">=</span> <span class="n">metadataG</span><span class="p">[</span><span class="n">metadataG</span><span class="p">[</span><span class="s1">&#39;type&#39;</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;G6&#39;</span><span class="p">]</span>
<span class="n">ax</span> <span class="o">=</span> <span class="n">G6Data</span><span class="o">.</span><span class="n">groupby</span><span class="p">([</span><span class="s1">&#39;Date&#39;</span><span class="p">,</span><span class="s1">&#39;plot_name&#39;</span><span class="p">])</span><span class="o">.</span><span class="n">sum</span><span class="p">()[</span><span class="s1">&#39;pLantAligned&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">unstack</span><span class="p">()</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">ax</span><span class="o">=</span><span class="n">ax</span><span class="p">,</span><span class="n">title</span><span class="o">=</span><span class="s2">&quot;Seasonal Perctage of reads aligning to Micanthus Assembly&quot;</span><span class="p">,</span><span class="n">fontsize</span><span class="o">=</span><span class="mi">12</span><span class="p">);</span>
<span class="n">ax</span><span class="o">.</span><span class="n">set_ylabel</span><span class="p">(</span><span class="s2">&quot;% Reads&quot;</span><span class="p">,</span><span class="n">fontsize</span><span class="o">=</span><span class="mi">14</span><span class="p">)</span>
<span class="n">ax</span><span class="o">.</span><span class="n">set_ylim</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="mi">100</span><span class="p">)</span>
<span class="c1"># fig = ax.get_figure()</span>
<span class="c1"># fig.savefig(&#39;images/MiscanPlantReads.png&#39;)</span>
</pre></div>

    </div>
</div>
</div>

  </div>
<div class="cell border-box-sizing text_cell rendered"><div class="inner_cell">
<div class="text_cell_render border-box-sizing rendered_html">
<h3 id="Remove-Human-Disease-Pathway-related-rows">Remove Human Disease Pathway related rows<a class="anchor-link" href="#Remove-Human-Disease-Pathway-related-rows">&#182;</a></h3>
</div>
</div>
</div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">allSampleCounts</span> <span class="o">=</span> <span class="n">allSampleCounts</span><span class="p">[</span><span class="n">allSampleCounts</span><span class="o">.</span><span class="n">Level1</span> <span class="o">!=</span> <span class="s2">&quot;Human Diseases&quot;</span><span class="p">]</span>
<span class="n">allSampleCounts</span><span class="o">.</span><span class="n">shape</span>
</pre></div>

    </div>
</div>
</div>

  </div>
<div class="cell border-box-sizing text_cell rendered"><div class="inner_cell">
<div class="text_cell_render border-box-sizing rendered_html">
<h3 id="Normalize-by-total-reads-and-log-transform">Normalize by total reads and log transform<a class="anchor-link" href="#Normalize-by-total-reads-and-log-transform">&#182;</a></h3>
</div>
</div>
</div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="kn">from</span> <span class="nn">numpy</span> <span class="k">import</span> <span class="n">log</span><span class="p">,</span> <span class="n">nan</span>
<span class="k">for</span> <span class="n">sample</span> <span class="ow">in</span> <span class="n">metadataG</span><span class="o">.</span><span class="n">index</span><span class="p">:</span>
    <span class="n">allSampleCounts</span><span class="p">[</span><span class="n">sample</span><span class="p">]</span><span class="o">=</span> <span class="o">-</span><span class="n">log</span><span class="p">(</span><span class="n">allSampleCounts</span><span class="p">[</span><span class="n">sample</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">nan</span><span class="p">)</span><span class="o">/</span><span class="n">metadataG</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="n">sample</span><span class="p">,</span><span class="s2">&quot;total_reads&quot;</span><span class="p">])</span>
<span class="k">for</span> <span class="n">sample</span> <span class="ow">in</span> <span class="n">metadataG</span><span class="o">.</span><span class="n">index</span><span class="p">:</span> <span class="n">allSampleCounts</span><span class="p">[</span><span class="n">sample</span><span class="p">]</span><span class="o">=</span> <span class="n">allSampleCounts</span><span class="p">[</span><span class="n">sample</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="n">nan</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span>
<span class="n">allSampleCounts</span><span class="o">.</span><span class="n">head</span><span class="p">()</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">allSampleCounts</span><span class="o">.</span><span class="n">head</span><span class="p">()</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">allSampleCounts</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="k">for</span> <span class="n">level</span> <span class="ow">in</span> <span class="p">[</span><span class="s2">&quot;Level1&quot;</span><span class="p">,</span><span class="s2">&quot;Level2&quot;</span><span class="p">,</span><span class="s2">&quot;Level3&quot;</span><span class="p">]:</span>
    <span class="n">outfile</span> <span class="o">=</span> <span class="s2">&quot;annotations/</span><span class="si">%s</span><span class="s2">_CountTable_logged2.tsv&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">level</span><span class="p">)</span>
    <span class="n">levelDF</span> <span class="o">=</span> <span class="n">allSampleCounts</span><span class="o">.</span><span class="n">groupby</span><span class="p">([</span><span class="n">level</span><span class="p">])</span><span class="o">.</span><span class="n">sum</span><span class="p">()</span>
    <span class="n">levelDF</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span><span class="n">outfile</span><span class="p">,</span><span class="n">sep</span><span class="o">=</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">fig</span><span class="p">,</span> <span class="n">ax</span> <span class="o">=</span> <span class="n">plt</span><span class="o">.</span><span class="n">subplots</span><span class="p">(</span><span class="n">figsize</span><span class="o">=</span><span class="p">(</span><span class="mi">15</span><span class="p">,</span><span class="mi">7</span><span class="p">))</span>
<span class="c1"># use unstack()</span>
<span class="n">data</span><span class="o">.</span><span class="n">groupby</span><span class="p">([</span><span class="s1">&#39;date&#39;</span><span class="p">,</span><span class="s1">&#39;type&#39;</span><span class="p">])</span><span class="o">.</span><span class="n">count</span><span class="p">()[</span><span class="s1">&#39;amount&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">unstack</span><span class="p">()</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">ax</span><span class="o">=</span><span class="n">ax</span><span class="p">)</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">colors</span> <span class="o">=</span> <span class="p">[</span><span class="s2">&quot;#74C476&quot;</span><span class="p">,</span> <span class="s2">&quot;#f26d07&quot;</span><span class="p">,</span><span class="s2">&quot;#794955&quot;</span><span class="p">]</span>
<span class="n">G5_metadata</span> <span class="o">=</span> <span class="n">metadataG</span><span class="p">[</span><span class="n">metadataG</span><span class="o">.</span><span class="n">type</span> <span class="o">==</span> <span class="s2">&quot;G5&quot;</span><span class="p">]</span>
<span class="n">G6_metadata</span> <span class="o">=</span> <span class="n">metadataG</span><span class="p">[</span><span class="n">metadataG</span><span class="o">.</span><span class="n">type</span> <span class="o">==</span> <span class="s2">&quot;G6&quot;</span><span class="p">]</span>

<span class="n">ax</span> <span class="o">=</span> <span class="n">G5_metadata</span><span class="o">.</span><span class="n">loc</span><span class="p">[:,[</span><span class="s1">&#39;Plant Reads&#39;</span><span class="p">,</span><span class="s1">&#39;Fungal Reads&#39;</span><span class="p">,</span> <span class="s1">&#39;Remaining&#39;</span><span class="p">]]</span><span class="o">.</span><span class="n">plot</span><span class="o">.</span><span class="n">bar</span><span class="p">(</span><span class="n">stacked</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">color</span><span class="o">=</span><span class="n">colors</span><span class="p">,</span> <span class="n">figsize</span><span class="o">=</span><span class="p">(</span><span class="mi">14</span><span class="p">,</span><span class="mi">7</span><span class="p">))</span>
<span class="n">ax</span><span class="o">.</span><span class="n">set_ylabel</span><span class="p">(</span><span class="s2">&quot;Read Count&quot;</span><span class="p">,</span><span class="n">fontsize</span><span class="o">=</span><span class="mi">12</span><span class="p">)</span>
<span class="n">ax</span><span class="o">.</span><span class="n">set_ylim</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="mi">16000000</span><span class="p">)</span>

<span class="n">fig</span> <span class="o">=</span> <span class="n">ax</span><span class="o">.</span><span class="n">get_figure</span><span class="p">()</span>
<span class="n">fig</span><span class="o">.</span><span class="n">savefig</span><span class="p">(</span><span class="s1">&#39;images/MiscanthusBarCombined.png&#39;</span><span class="p">)</span>
<span class="n">ax</span> <span class="o">=</span> <span class="n">G6_metadata</span><span class="o">.</span><span class="n">loc</span><span class="p">[:,[</span><span class="s1">&#39;Plant Reads&#39;</span><span class="p">,</span><span class="s1">&#39;Fungal Reads&#39;</span><span class="p">,</span> <span class="s1">&#39;Remaining&#39;</span><span class="p">]]</span><span class="o">.</span><span class="n">plot</span><span class="o">.</span><span class="n">bar</span><span class="p">(</span><span class="n">stacked</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">color</span><span class="o">=</span><span class="n">colors</span><span class="p">,</span> <span class="n">figsize</span><span class="o">=</span><span class="p">(</span><span class="mi">14</span><span class="p">,</span><span class="mi">7</span><span class="p">))</span>
<span class="n">ax</span><span class="o">.</span><span class="n">set_ylabel</span><span class="p">(</span><span class="s2">&quot;Read Count (Millions)&quot;</span><span class="p">,</span><span class="n">fontsize</span><span class="o">=</span><span class="mi">12</span><span class="p">)</span>
<span class="n">fig</span> <span class="o">=</span> <span class="n">ax</span><span class="o">.</span><span class="n">get_figure</span><span class="p">()</span>
<span class="n">fig</span><span class="o">.</span><span class="n">savefig</span><span class="p">(</span><span class="s1">&#39;images/SwitchgrassBarCombined.png&#39;</span><span class="p">)</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">metaG_Reads</span> <span class="o">=</span> <span class="n">read_csv</span><span class="p">(</span><span class="s2">&quot;mapping/metaG/fullAssembly/multiqc_data/multiqc_bowtie2.txt&quot;</span><span class="p">,</span><span class="n">sep</span><span class="o">=</span><span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">)</span>
<span class="k">for</span> <span class="nb">id</span> <span class="ow">in</span> <span class="n">metaG_Reads</span><span class="o">.</span><span class="n">index</span><span class="p">:</span> <span class="n">metaG_Reads</span><span class="o">.</span><span class="n">at</span><span class="p">[</span><span class="nb">id</span><span class="p">,</span><span class="s2">&quot;Sample&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="n">metaG_Reads</span><span class="o">.</span><span class="n">at</span><span class="p">[</span><span class="nb">id</span><span class="p">,</span><span class="s2">&quot;Sample&quot;</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;.fungal.stat&quot;</span><span class="p">,</span><span class="s2">&quot;&quot;</span><span class="p">)</span>
<span class="n">metaG_Reads</span><span class="o">.</span><span class="n">set_index</span><span class="p">(</span><span class="s2">&quot;Sample&quot;</span><span class="p">,</span><span class="n">inplace</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>

<span class="n">metadataG</span> <span class="o">=</span> <span class="n">merge</span><span class="p">(</span><span class="n">metadataG</span><span class="p">,</span><span class="n">metaG_Reads</span><span class="p">,</span><span class="n">left_index</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span><span class="n">right_index</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="n">metadataG</span><span class="o">.</span><span class="n">sort_values</span><span class="p">(</span><span class="s2">&quot;Date&quot;</span><span class="p">,</span><span class="n">inplace</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">metadataG</span> <span class="o">=</span> <span class="n">metadataG</span><span class="p">[</span><span class="n">metadataG</span><span class="p">[</span><span class="s1">&#39;type&#39;</span><span class="p">]</span><span class="o">==</span><span class="s2">&quot;G5&quot;</span><span class="p">]</span> <span class="c1"># SWITCHGRASS Only</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">metadataG</span><span class="p">[</span><span class="s2">&quot;total_reads&quot;</span><span class="p">]</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">kind</span><span class="o">=</span><span class="s1">&#39;bar&#39;</span><span class="p">,</span><span class="n">ax</span><span class="o">=</span><span class="n">plt</span><span class="o">.</span><span class="n">subplot</span><span class="p">(</span><span class="mi">121</span><span class="p">),</span><span class="n">figsize</span><span class="o">=</span><span class="p">(</span><span class="mi">30</span><span class="p">,</span><span class="mi">10</span><span class="p">),</span><span class="n">title</span><span class="o">=</span><span class="s2">&quot;SG MetaG after host removal&quot;</span><span class="p">,</span><span class="n">color</span><span class="o">=</span><span class="s1">&#39;orange&#39;</span><span class="p">)</span>
<span class="n">metadataT</span><span class="p">[</span><span class="s2">&quot;total_reads&quot;</span><span class="p">]</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">kind</span><span class="o">=</span><span class="s1">&#39;bar&#39;</span><span class="p">,</span><span class="n">ax</span><span class="o">=</span><span class="n">plt</span><span class="o">.</span><span class="n">subplot</span><span class="p">(</span><span class="mi">122</span><span class="p">),</span><span class="n">figsize</span><span class="o">=</span><span class="p">(</span><span class="mi">30</span><span class="p">,</span><span class="mi">10</span><span class="p">),</span><span class="n">title</span><span class="o">=</span><span class="s2">&quot;SG MetaT after host removal&quot;</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">show</span><span class="p">()</span>
</pre></div>

    </div>
</div>
</div>

  </div>
<div class="cell border-box-sizing text_cell rendered"><div class="inner_cell">
<div class="text_cell_render border-box-sizing rendered_html">
<h1 id="Creating-links-to-the-raw-data-files-from-JGI">Creating links to the raw data files from JGI<a class="anchor-link" href="#Creating-links-to-the-raw-data-files-from-JGI">&#182;</a></h1>
</div>
</div>
</div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="kn">from</span> <span class="nn">os</span> <span class="k">import</span> <span class="n">listdir</span><span class="p">,</span> <span class="n">path</span><span class="p">,</span> <span class="n">system</span>
<span class="n">rawFiles</span> <span class="o">=</span> <span class="p">{}</span>
<span class="n">baseDir</span> <span class="o">=</span> <span class="s2">&quot;/mnt/research/ShadeLab/Sequence/raw_sequence/GLBRC/metagenomes/&quot;</span>
<span class="n">dirs</span> <span class="o">=</span> <span class="n">listdir</span><span class="p">(</span><span class="n">baseDir</span><span class="p">)</span>
<span class="k">for</span> <span class="n">dirName</span> <span class="ow">in</span> <span class="n">dirs</span><span class="p">:</span>
    <span class="n">rawDir</span> <span class="o">=</span> <span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">baseDir</span><span class="p">,</span><span class="n">dirName</span><span class="p">,</span><span class="s2">&quot;Raw_Data/&quot;</span><span class="p">)</span>
    <span class="n">fastq</span> <span class="o">=</span> <span class="n">listdir</span><span class="p">(</span><span class="n">rawDir</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
    <span class="n">rawFiles</span><span class="p">[</span><span class="n">fastq</span><span class="p">]</span> <span class="o">=</span> <span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">rawDir</span><span class="p">,</span><span class="n">fastq</span><span class="p">)</span>
<span class="n">metaGUnpaired</span> <span class="o">=</span> <span class="s2">&quot;/mnt/research/ShadeLab/GLBRC/mapping/metaG/unpaired/</span><span class="si">%s</span><span class="s2">.fastq.gz&quot;</span>
    
<span class="k">for</span> <span class="n">readFName</span><span class="p">,</span><span class="n">row</span> <span class="ow">in</span> <span class="n">metadata</span><span class="o">.</span><span class="n">iterrows</span><span class="p">():</span>
    <span class="k">if</span> <span class="n">readFName</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">rawFiles</span><span class="p">:</span>
        <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;No fastq for &quot;</span><span class="o">+</span><span class="n">readFileName</span><span class="p">)</span>
        <span class="k">continue</span>
    <span class="n">system</span><span class="p">(</span><span class="s2">&quot;ln -s </span><span class="si">%s</span><span class="s2"> </span><span class="si">%s</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">rawFiles</span><span class="p">[</span><span class="n">readFName</span><span class="p">],</span><span class="n">metaGUnpaired</span> <span class="o">%</span><span class="p">(</span><span class="n">row</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="s1">&#39;nucleic_acid_name&#39;</span><span class="p">])))</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">fig</span><span class="p">,</span> <span class="n">ax</span> <span class="o">=</span> <span class="n">plt</span><span class="o">.</span><span class="n">subplots</span><span class="p">(</span><span class="n">figsize</span><span class="o">=</span><span class="p">(</span><span class="mi">8</span><span class="p">,</span><span class="mi">5</span><span class="p">))</span>
<span class="n">G5Data</span> <span class="o">=</span> <span class="n">metadataG</span><span class="p">[</span><span class="n">metadataG</span><span class="p">[</span><span class="s1">&#39;type&#39;</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;G5&#39;</span><span class="p">]</span>
<span class="n">G5Data</span><span class="o">.</span><span class="n">groupby</span><span class="p">([</span><span class="s1">&#39;Date&#39;</span><span class="p">,</span><span class="s1">&#39;plot_name&#39;</span><span class="p">])</span><span class="o">.</span><span class="n">sum</span><span class="p">()[</span><span class="s1">&#39;percFungalAligned&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">unstack</span><span class="p">()</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">ax</span><span class="o">=</span><span class="n">ax</span><span class="p">,</span><span class="n">title</span><span class="o">=</span><span class="s2">&quot;Seasonal Perctages of Reads Aligning to Combined Fungal Assemblies&quot;</span><span class="p">);</span>
<span class="n">ax</span><span class="o">.</span><span class="n">set_ylabel</span><span class="p">(</span><span class="s2">&quot;% Reads&quot;</span><span class="p">,</span><span class="n">fontsize</span><span class="o">=</span><span class="mi">14</span><span class="p">)</span>
<span class="n">ax</span><span class="o">.</span><span class="n">set_ylim</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="mi">10</span><span class="p">)</span>
<span class="n">fig</span> <span class="o">=</span> <span class="n">ax</span><span class="o">.</span><span class="n">get_figure</span><span class="p">()</span>
<span class="n">fig</span><span class="o">.</span><span class="n">savefig</span><span class="p">(</span><span class="s1">&#39;images/SwitchgrassFungalAlign.png&#39;</span><span class="p">)</span>
</pre></div>

    </div>
</div>
</div>

  </div>
<div class="cell border-box-sizing text_cell rendered"><div class="inner_cell">
<div class="text_cell_render border-box-sizing rendered_html">
<p><h2><a id="analysis">Sequence Mapping Overview</a></h2></p>
<h4>Host organism reads removal</h4>
</div>
</div>
</div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">hostMapping</span> <span class="o">=</span> <span class="n">read_csv</span><span class="p">(</span><span class="s2">&quot;mapping/metaG/fullAssembly/multiqc_data/multiqc_bowtie2.txt&quot;</span><span class="p">,</span><span class="n">sep</span><span class="o">=</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
<span class="n">hostMapping</span><span class="o">.</span><span class="n">set_index</span><span class="p">(</span><span class="s2">&quot;Sample&quot;</span><span class="p">,</span><span class="n">inplace</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="n">hostMapping</span><span class="p">[</span><span class="s1">&#39;type&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s2">&quot;&quot;</span>
<span class="k">for</span> <span class="nb">id</span> <span class="ow">in</span> <span class="n">hostMapping</span><span class="o">.</span><span class="n">index</span><span class="p">:</span> <span class="n">hostMapping</span><span class="o">.</span><span class="n">at</span><span class="p">[</span><span class="nb">id</span><span class="p">,</span><span class="s2">&quot;type&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="nb">id</span><span class="p">[</span><span class="mi">0</span><span class="p">:</span><span class="mi">2</span><span class="p">]</span>
<span class="n">hostMapping</span><span class="p">[</span><span class="s2">&quot;sample_name&quot;</span><span class="p">]</span><span class="o">=</span><span class="s2">&quot;&quot;</span>
<span class="k">for</span> <span class="nb">id</span> <span class="ow">in</span> <span class="n">hostMapping</span><span class="o">.</span><span class="n">index</span><span class="p">:</span> <span class="n">hostMapping</span><span class="o">.</span><span class="n">at</span><span class="p">[</span><span class="nb">id</span><span class="p">,</span><span class="s2">&quot;sample_name&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="nb">id</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;.stat&quot;</span><span class="p">,</span><span class="s2">&quot;&quot;</span><span class="p">)</span>
<span class="n">hostMapping</span><span class="o">.</span><span class="n">set_index</span><span class="p">(</span><span class="s2">&quot;sample_name&quot;</span><span class="p">,</span><span class="n">inplace</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="n">hostMapping</span><span class="o">.</span><span class="n">head</span><span class="p">()</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">SGData</span> <span class="o">=</span> <span class="n">hostMapping</span><span class="p">[</span><span class="n">hostMapping</span><span class="p">[</span><span class="s1">&#39;type&#39;</span><span class="p">]</span><span class="o">==</span><span class="s1">&#39;G5&#39;</span><span class="p">]</span>
<span class="n">MiscanData</span> <span class="o">=</span> <span class="n">hostMapping</span><span class="p">[</span><span class="n">hostMapping</span><span class="p">[</span><span class="s1">&#39;type&#39;</span><span class="p">]</span><span class="o">==</span><span class="s1">&#39;G6&#39;</span><span class="p">]</span>

<span class="n">sgTotal</span> <span class="o">=</span> <span class="n">SGData</span><span class="p">[</span><span class="s1">&#39;total_reads&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">sum</span><span class="p">()</span>
<span class="n">miscanTotatl</span> <span class="o">=</span> <span class="n">MiscanData</span><span class="p">[</span><span class="s1">&#39;total_reads&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">sum</span><span class="p">()</span>

<span class="n">sgBact</span> <span class="o">=</span> <span class="n">SGData</span><span class="p">[</span><span class="s1">&#39;paired_aligned_none&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">sum</span><span class="p">()</span>
<span class="n">miscanBact</span> <span class="o">=</span> <span class="n">MiscanData</span><span class="p">[</span><span class="s1">&#39;paired_aligned_none&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">sum</span><span class="p">()</span>

<span class="p">(</span><span class="n">sgTotal</span><span class="o">-</span><span class="n">sgBact</span><span class="p">)</span><span class="o">/</span><span class="n">sgTotal</span><span class="o">*</span><span class="mi">100</span>

<span class="p">(</span><span class="n">miscanTotatl</span><span class="o">-</span><span class="n">miscanBact</span><span class="p">)</span><span class="o">/</span><span class="n">miscanTotatl</span><span class="o">*</span><span class="mi">100</span>

<span class="n">comma</span><span class="p">(</span><span class="n">SGData</span><span class="p">[</span><span class="s1">&#39;paired_aligned_none&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">sum</span><span class="p">()</span> <span class="o">+</span><span class="n">MiscanData</span><span class="p">[</span><span class="s1">&#39;paired_aligned_none&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">sum</span><span class="p">())</span>
</pre></div>

    </div>
</div>
</div>

  </div>
<div class="cell border-box-sizing text_cell rendered"><div class="inner_cell">
<div class="text_cell_render border-box-sizing rendered_html">
<h4 id="Alignment-of-non-host-related-reads-to-metagenomic-assembly">Alignment of non-host related reads to metagenomic assembly<a class="anchor-link" href="#Alignment-of-non-host-related-reads-to-metagenomic-assembly">&#182;</a></h4>
</div>
</div>
</div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">seqMapping</span> <span class="o">=</span> <span class="n">read_csv</span><span class="p">(</span><span class="s2">&quot;mapping/metaG/fullAssembly/multiqc_data/multiqc_bowtie2.txt&quot;</span><span class="p">,</span><span class="n">sep</span><span class="o">=</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
<span class="n">seqMapping</span><span class="o">.</span><span class="n">set_index</span><span class="p">(</span><span class="s2">&quot;Sample&quot;</span><span class="p">,</span><span class="n">inplace</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="n">seqMapping</span><span class="p">[</span><span class="s1">&#39;type&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s2">&quot;&quot;</span>
<span class="k">for</span> <span class="nb">id</span> <span class="ow">in</span> <span class="n">seqMapping</span><span class="o">.</span><span class="n">index</span><span class="p">:</span> <span class="n">seqMapping</span><span class="o">.</span><span class="n">at</span><span class="p">[</span><span class="nb">id</span><span class="p">,</span><span class="s2">&quot;type&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="nb">id</span><span class="p">[</span><span class="mi">0</span><span class="p">:</span><span class="mi">2</span><span class="p">]</span>
<span class="n">seqMapping</span><span class="p">[</span><span class="s2">&quot;sample_name&quot;</span><span class="p">]</span><span class="o">=</span><span class="s2">&quot;&quot;</span>
<span class="k">for</span> <span class="nb">id</span> <span class="ow">in</span> <span class="n">seqMapping</span><span class="o">.</span><span class="n">index</span><span class="p">:</span> <span class="n">seqMapping</span><span class="o">.</span><span class="n">at</span><span class="p">[</span><span class="nb">id</span><span class="p">,</span><span class="s2">&quot;sample_name&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="nb">id</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;.stat&quot;</span><span class="p">,</span><span class="s2">&quot;&quot;</span><span class="p">)</span>
<span class="n">seqMapping</span><span class="o">.</span><span class="n">set_index</span><span class="p">(</span><span class="s2">&quot;sample_name&quot;</span><span class="p">,</span><span class="n">inplace</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="n">seqMapping</span><span class="o">.</span><span class="n">head</span><span class="p">()</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">SGData</span> <span class="o">=</span> <span class="n">seqMapping</span><span class="p">[</span><span class="n">hostMapping</span><span class="p">[</span><span class="s1">&#39;type&#39;</span><span class="p">]</span><span class="o">==</span><span class="s1">&#39;G5&#39;</span><span class="p">]</span>
<span class="n">MiscanData</span> <span class="o">=</span> <span class="n">seqMapping</span><span class="p">[</span><span class="n">hostMapping</span><span class="p">[</span><span class="s1">&#39;type&#39;</span><span class="p">]</span><span class="o">==</span><span class="s1">&#39;G6&#39;</span><span class="p">]</span>

<span class="n">sgTotal</span> <span class="o">=</span> <span class="n">SGData</span><span class="p">[</span><span class="s1">&#39;total_reads&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">sum</span><span class="p">()</span>
<span class="n">miscanTotatl</span> <span class="o">=</span> <span class="n">MiscanData</span><span class="p">[</span><span class="s1">&#39;total_reads&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">sum</span><span class="p">()</span>

<span class="n">sgBact</span> <span class="o">=</span> <span class="n">SGData</span><span class="p">[</span><span class="s1">&#39;paired_aligned_none&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">sum</span><span class="p">()</span>
<span class="n">miscanBact</span> <span class="o">=</span> <span class="n">MiscanData</span><span class="p">[</span><span class="s1">&#39;paired_aligned_none&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">sum</span><span class="p">()</span>

<span class="nb">print</span><span class="p">(</span><span class="s1">&#39;SG </span><span class="si">%%</span><span class="s1"> aligned: </span><span class="si">%.2f</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">((</span><span class="n">sgTotal</span><span class="o">-</span><span class="n">sgBact</span><span class="p">)</span><span class="o">/</span><span class="n">sgTotal</span><span class="o">*</span><span class="mi">100</span><span class="p">),</span><span class="n">comma</span><span class="p">(</span><span class="n">sgTotal</span><span class="p">))</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Miscanthus </span><span class="si">%%</span><span class="s1"> aligned: </span><span class="si">%.2f</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">((</span><span class="n">miscanTotatl</span><span class="o">-</span><span class="n">miscanBact</span><span class="p">)</span><span class="o">/</span><span class="n">miscanTotatl</span><span class="o">*</span><span class="mi">100</span><span class="p">),</span><span class="n">comma</span><span class="p">(</span><span class="n">miscanTotatl</span><span class="p">))</span>
<span class="nb">print</span><span class="p">(</span><span class="n">comma</span><span class="p">(</span><span class="n">SGData</span><span class="p">[</span><span class="s1">&#39;paired_aligned_none&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">sum</span><span class="p">()</span> <span class="o">+</span><span class="n">MiscanData</span><span class="p">[</span><span class="s1">&#39;paired_aligned_none&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">sum</span><span class="p">()))</span>

<span class="c1">#MetaG</span>
<span class="c1"># metaG = read_csv(&quot;mapping/metaG/annotatedContigs/logs/multiqc_data/mqc_trimmomatic_plot_1.txt&quot;,sep=&quot;\t&quot;)</span>
<span class="c1"># metaG.set_index(&#39;Sample&#39;,inplace=True)</span>
<span class="c1"># print(comma(metaG[&#39;Surviving Reads&#39;].sum()))</span>

<span class="c1"># metaT = read_csv(&quot;mapping/metaT/fullAssembly/logs/multiqc_data/multiqc_trimmomatic.txt&quot;,sep=&quot;\t&quot;)</span>
<span class="c1"># metaT.set_index(&#39;Sample&#39;,inplace=True)</span>
<span class="c1"># print(comma(metaT[&#39;surviving&#39;].sum())</span>

<span class="c1"># metaT[&#39;Base&#39;],metaG[&#39;Base&#39;] = &#39;&#39;,&#39;&#39;</span>

<span class="c1"># for sampleID in metaG.index:</span>
<span class="c1">#     metaG.at[sampleID,&#39;Base&#39;] = sampleID[:sampleID.rfind(&#39;_&#39;)]</span>
<span class="c1"># for sampleID in metaT.index:</span>
<span class="c1">#     metaT.at[sampleID,&#39;Base&#39;] = sampleID[:sampleID.rfind(&#39;_&#39;)]</span>

<span class="c1"># metaT.set_index(&quot;Base&quot;,inplace=True)</span>
<span class="c1"># metaG.set_index(&quot;Base&quot;,inplace=True)</span>

<span class="c1"># comma(metaT[&#39;surviving&#39;].sum()-metaG[&#39;Surviving Reads&#39;].sum())</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="c1"># for sampleID in ids.intersection(ids2):</span>
<span class="c1">#     print(sampleID,&#39;\t&#39;,comma(int(metaT.at[sampleID,&#39;surviving&#39;])),&#39;\t&#39;,comma(int(metaG.at[sampleID,&#39;Surviving Reads&#39;])))</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">data</span> <span class="o">=</span> <span class="n">read_csv</span><span class="p">(</span><span class="s2">&quot;mapping/metaG/annotatedContigs/logs/multiqc_data/mqc_bowtie2_pe_plot_1.txt&quot;</span><span class="p">,</span><span class="n">sep</span><span class="o">=</span><span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">)</span>
<span class="n">data</span><span class="p">[</span><span class="s2">&quot;TotalSampleReads&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="n">data</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
<span class="c1">#data[[&quot;PE mapped uniquely&quot;,&quot;PE mapped discordantly uniquely&quot;,&quot;PE multimapped&quot;]]/data[&quot;TotalSampleReads&quot;] </span>
<span class="nb">print</span><span class="p">(</span><span class="s2">&quot;(</span><span class="si">%i</span><span class="s2">, </span><span class="si">%i</span><span class="s2">)&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">data</span><span class="o">.</span><span class="n">shape</span><span class="p">,</span> <span class="n">metadata</span><span class="o">.</span><span class="n">shape</span><span class="p">))</span>
<span class="n">data</span><span class="o">.</span><span class="n">head</span><span class="p">()</span>
</pre></div>

    </div>
</div>
</div>

  </div>
<div class="cell border-box-sizing text_cell rendered"><div class="inner_cell">
<div class="text_cell_render border-box-sizing rendered_html">
<h1 id="Microbe-Census-(single-copy-gene-counts)">Microbe Census (single copy gene counts)<a class="anchor-link" href="#Microbe-Census-(single-copy-gene-counts)">&#182;</a></h1>
</div>
</div>
</div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="kn">from</span> <span class="nn">os</span> <span class="k">import</span> <span class="n">listdir</span>
<span class="n">scc_path</span><span class="o">=</span><span class="s2">&quot;mapping/metaG/fullAssembly/singleCopyGeneCounts/&quot;</span>
<span class="n">files</span> <span class="o">=</span> <span class="n">listdir</span><span class="p">(</span><span class="n">scc_path</span><span class="p">)</span>
<span class="n">metadata</span><span class="p">[</span><span class="s2">&quot;genome_equivalents&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="mf">0.0</span>
<span class="n">metadata</span><span class="p">[</span><span class="s2">&quot;average_genome_size&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="mf">0.0</span>
<span class="n">metadata</span><span class="p">[</span><span class="s2">&quot;total_reads&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span>

<span class="k">for</span> <span class="n">fname</span> <span class="ow">in</span> <span class="n">files</span><span class="p">:</span>
    <span class="n">sampleID</span> <span class="o">=</span> <span class="n">fname</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;.txt&quot;</span><span class="p">,</span><span class="s2">&quot;&quot;</span><span class="p">)</span>
    <span class="n">metadata</span><span class="o">.</span><span class="n">at</span><span class="p">[</span><span class="n">sampleID</span><span class="p">,</span><span class="s2">&quot;total_reads&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="n">seqMapping</span><span class="o">.</span><span class="n">at</span><span class="p">[</span><span class="n">sampleID</span><span class="p">,</span><span class="s2">&quot;total_reads&quot;</span><span class="p">]</span>
    <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">open</span><span class="p">(</span><span class="n">scc_path</span><span class="o">+</span><span class="n">fname</span><span class="p">):</span>
        <span class="k">if</span> <span class="s2">&quot;average_genome_size&quot;</span> <span class="ow">in</span> <span class="n">line</span><span class="p">:</span>
<span class="c1">#             print(line.strip().split(&quot;\t&quot;))</span>
            <span class="n">ags</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">)[</span><span class="mi">1</span><span class="p">])</span>
            <span class="n">metadata</span><span class="o">.</span><span class="n">at</span><span class="p">[</span><span class="n">sampleID</span><span class="p">,</span><span class="s2">&quot;average_genome_size&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="n">ags</span>
        <span class="k">elif</span> <span class="s2">&quot;genome_equivalents&quot;</span> <span class="ow">in</span> <span class="n">line</span><span class="p">:</span> 
            <span class="n">ge</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">)[</span><span class="mi">1</span><span class="p">])</span>
            <span class="n">metadata</span><span class="o">.</span><span class="n">at</span><span class="p">[</span><span class="n">sampleID</span><span class="p">,</span><span class="s2">&quot;genome_equivalents&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="n">ge</span>
            
            
<span class="n">metadata</span><span class="o">.</span><span class="n">head</span><span class="p">(</span><span class="mi">20</span><span class="p">)</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">df</span> <span class="o">=</span> <span class="n">metadata</span><span class="o">.</span><span class="n">groupby</span><span class="p">([</span><span class="s1">&#39;Date&#39;</span><span class="p">])</span><span class="o">.</span><span class="n">mean</span><span class="p">()</span>
<span class="n">df</span><span class="p">[</span><span class="s2">&quot;average_genome_size&quot;</span><span class="p">]</span><span class="o">=</span><span class="n">df</span><span class="p">[</span><span class="s2">&quot;average_genome_size&quot;</span><span class="p">]</span><span class="o">/</span><span class="mf">1000000.0</span>
<span class="n">df</span><span class="p">[</span><span class="s2">&quot;total_reads&quot;</span><span class="p">]</span><span class="o">=</span><span class="n">df</span><span class="p">[</span><span class="s2">&quot;total_reads&quot;</span><span class="p">]</span><span class="o">/</span><span class="mf">25000.0</span>
<span class="n">df</span><span class="o">.</span><span class="n">reset_index</span><span class="p">()</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">x</span><span class="o">=</span><span class="s2">&quot;Date&quot;</span><span class="p">,</span> <span class="n">y</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;genome_equivalents&quot;</span><span class="p">,</span> <span class="s2">&quot;average_genome_size&quot;</span><span class="p">,</span><span class="s2">&quot;total_reads&quot;</span><span class="p">],</span> <span class="n">kind</span><span class="o">=</span><span class="s2">&quot;bar&quot;</span><span class="p">,</span><span class="n">figsize</span><span class="o">=</span><span class="p">(</span><span class="mi">15</span><span class="p">,</span><span class="mi">8</span><span class="p">));</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span> 
</pre></div>

    </div>
</div>
</div>

  </div>
<div class="cell border-box-sizing text_cell rendered"><div class="inner_cell">
<div class="text_cell_render border-box-sizing rendered_html">
<h3 id="For-MetaT">For MetaT<a class="anchor-link" href="#For-MetaT">&#182;</a></h3>
</div>
</div>
</div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">seqMapping</span> <span class="o">=</span> <span class="n">read_csv</span><span class="p">(</span><span class="s2">&quot;mapping/metaT/fullAssembly/multiqc_data/multiqc_bowtie2.txt&quot;</span><span class="p">,</span><span class="n">sep</span><span class="o">=</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
<span class="n">seqMapping</span><span class="o">.</span><span class="n">set_index</span><span class="p">(</span><span class="s2">&quot;Sample&quot;</span><span class="p">,</span><span class="n">inplace</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="n">seqMapping</span><span class="p">[</span><span class="s1">&#39;type&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s2">&quot;&quot;</span>
<span class="k">for</span> <span class="nb">id</span> <span class="ow">in</span> <span class="n">seqMapping</span><span class="o">.</span><span class="n">index</span><span class="p">:</span> <span class="n">seqMapping</span><span class="o">.</span><span class="n">at</span><span class="p">[</span><span class="nb">id</span><span class="p">,</span><span class="s2">&quot;type&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="nb">id</span><span class="p">[</span><span class="mi">0</span><span class="p">:</span><span class="mi">2</span><span class="p">]</span>
<span class="n">seqMapping</span><span class="p">[</span><span class="s2">&quot;sample_name&quot;</span><span class="p">]</span><span class="o">=</span><span class="s2">&quot;&quot;</span>
<span class="k">for</span> <span class="nb">id</span> <span class="ow">in</span> <span class="n">seqMapping</span><span class="o">.</span><span class="n">index</span><span class="p">:</span> <span class="n">seqMapping</span><span class="o">.</span><span class="n">at</span><span class="p">[</span><span class="nb">id</span><span class="p">,</span><span class="s2">&quot;sample_name&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="nb">id</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;.stat&quot;</span><span class="p">,</span><span class="s2">&quot;&quot;</span><span class="p">)</span>
<span class="n">seqMapping</span><span class="o">.</span><span class="n">set_index</span><span class="p">(</span><span class="s2">&quot;sample_name&quot;</span><span class="p">,</span><span class="n">inplace</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="n">seqMapping</span><span class="o">.</span><span class="n">head</span><span class="p">()</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="kn">from</span> <span class="nn">os</span> <span class="k">import</span> <span class="n">listdir</span>
<span class="n">scc_path</span><span class="o">=</span><span class="s2">&quot;mapping/metaT/fullAssembly/singleCopyGeneCounts/&quot;</span>
<span class="n">files</span> <span class="o">=</span> <span class="n">listdir</span><span class="p">(</span><span class="n">scc_path</span><span class="p">)</span>
<span class="n">metadata</span><span class="p">[</span><span class="s2">&quot;genome_equivalents&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="mf">0.0</span>
<span class="n">metadata</span><span class="p">[</span><span class="s2">&quot;average_genome_size&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="mf">0.0</span>
<span class="n">metadata</span><span class="p">[</span><span class="s2">&quot;total_reads&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span>

<span class="k">for</span> <span class="n">fname</span> <span class="ow">in</span> <span class="n">files</span><span class="p">:</span>
    <span class="n">sampleID</span> <span class="o">=</span> <span class="n">fname</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;.txt&quot;</span><span class="p">,</span><span class="s2">&quot;&quot;</span><span class="p">)</span>
    <span class="k">if</span> <span class="n">sampleID</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">seqMapping</span><span class="o">.</span><span class="n">index</span><span class="p">:</span>
        <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;Missing:&quot;</span><span class="p">,</span><span class="n">sampleID</span><span class="p">,</span><span class="n">fname</span><span class="p">)</span>
        <span class="k">continue</span>
    <span class="n">metadata</span><span class="o">.</span><span class="n">at</span><span class="p">[</span><span class="n">sampleID</span><span class="p">,</span><span class="s2">&quot;total_reads&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="n">seqMapping</span><span class="o">.</span><span class="n">at</span><span class="p">[</span><span class="n">sampleID</span><span class="p">,</span><span class="s2">&quot;total_reads&quot;</span><span class="p">]</span>
    <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">open</span><span class="p">(</span><span class="n">scc_path</span><span class="o">+</span><span class="n">fname</span><span class="p">):</span>
        <span class="k">if</span> <span class="s2">&quot;average_genome_size&quot;</span> <span class="ow">in</span> <span class="n">line</span><span class="p">:</span>
<span class="c1">#             print(line.strip().split(&quot;\t&quot;))</span>
            <span class="n">ags</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">)[</span><span class="mi">1</span><span class="p">])</span>
            <span class="n">metadata</span><span class="o">.</span><span class="n">at</span><span class="p">[</span><span class="n">sampleID</span><span class="p">,</span><span class="s2">&quot;average_genome_size&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="n">ags</span>
        <span class="k">elif</span> <span class="s2">&quot;genome_equivalents&quot;</span> <span class="ow">in</span> <span class="n">line</span><span class="p">:</span> 
            <span class="n">ge</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">)[</span><span class="mi">1</span><span class="p">])</span>
            <span class="n">metadata</span><span class="o">.</span><span class="n">at</span><span class="p">[</span><span class="n">sampleID</span><span class="p">,</span><span class="s2">&quot;genome_equivalents&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="n">ge</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">metadata</span><span class="o">.</span><span class="n">head</span><span class="p">()</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">df</span> <span class="o">=</span> <span class="n">metadata</span><span class="o">.</span><span class="n">groupby</span><span class="p">([</span><span class="s1">&#39;Date&#39;</span><span class="p">])</span><span class="o">.</span><span class="n">mean</span><span class="p">()</span>
<span class="n">df</span><span class="o">.</span><span class="n">sort_values</span><span class="p">(</span><span class="n">by</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;month&quot;</span><span class="p">],</span><span class="n">inplace</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="n">df</span><span class="p">[</span><span class="s2">&quot;average_genome_size&quot;</span><span class="p">]</span><span class="o">=</span><span class="n">df</span><span class="p">[</span><span class="s2">&quot;average_genome_size&quot;</span><span class="p">]</span><span class="o">/</span><span class="mf">10000.0</span>
<span class="n">df</span><span class="p">[</span><span class="s2">&quot;total_reads&quot;</span><span class="p">]</span><span class="o">=</span><span class="n">df</span><span class="p">[</span><span class="s2">&quot;total_reads&quot;</span><span class="p">]</span><span class="o">/</span><span class="mf">25000.0</span>
<span class="n">df</span><span class="o">.</span><span class="n">reset_index</span><span class="p">()</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">x</span><span class="o">=</span><span class="s2">&quot;Date&quot;</span><span class="p">,</span> <span class="n">y</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;genome_equivalents&quot;</span><span class="p">,</span> <span class="s2">&quot;average_genome_size&quot;</span><span class="p">,</span><span class="s2">&quot;total_reads&quot;</span><span class="p">],</span> <span class="n">kind</span><span class="o">=</span><span class="s2">&quot;bar&quot;</span><span class="p">,</span><span class="n">figsize</span><span class="o">=</span><span class="p">(</span><span class="mi">15</span><span class="p">,</span><span class="mi">8</span><span class="p">));</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">df</span><span class="o">=</span><span class="n">metadataG</span>

<span class="kn">import</span> <span class="nn">cufflinks</span> <span class="k">as</span> <span class="nn">cf</span>

<span class="nd">@interact</span>
<span class="k">def</span> <span class="nf">scatter_plot</span><span class="p">(</span><span class="n">x</span><span class="o">=</span><span class="nb">list</span><span class="p">(</span><span class="n">df</span><span class="o">.</span><span class="n">select_dtypes</span><span class="p">(</span><span class="s1">&#39;number&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">columns</span><span class="p">),</span> 
                 <span class="n">y</span><span class="o">=</span><span class="nb">list</span><span class="p">(</span><span class="n">df</span><span class="o">.</span><span class="n">select_dtypes</span><span class="p">(</span><span class="s1">&#39;number&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">columns</span><span class="p">)[</span><span class="mi">1</span><span class="p">:],</span>
                 <span class="n">theme</span><span class="o">=</span><span class="nb">list</span><span class="p">(</span><span class="n">cf</span><span class="o">.</span><span class="n">themes</span><span class="o">.</span><span class="n">THEMES</span><span class="o">.</span><span class="n">keys</span><span class="p">()),</span> 
                 <span class="n">colorscale</span><span class="o">=</span><span class="nb">list</span><span class="p">(</span><span class="n">cf</span><span class="o">.</span><span class="n">colors</span><span class="o">.</span><span class="n">_scales_names</span><span class="o">.</span><span class="n">keys</span><span class="p">())):</span>
    <span class="nb">print</span><span class="p">(</span><span class="n">x</span><span class="o">.</span><span class="n">title</span><span class="p">())</span>
    <span class="nb">print</span><span class="p">(</span><span class="n">y</span><span class="o">.</span><span class="n">title</span><span class="p">())</span>
    <span class="k">return</span> <span class="n">df</span><span class="o">.</span><span class="n">iplot</span><span class="p">(</span><span class="n">kind</span><span class="o">=</span><span class="s1">&#39;scatter&#39;</span><span class="p">,</span> <span class="n">x</span><span class="o">=</span><span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="o">=</span><span class="n">y</span><span class="p">,</span> <span class="n">mode</span><span class="o">=</span><span class="s1">&#39;markers&#39;</span><span class="p">,</span> 
             <span class="n">xTitle</span><span class="o">=</span><span class="n">x</span><span class="o">.</span><span class="n">title</span><span class="p">(),</span> <span class="n">yTitle</span><span class="o">=</span><span class="n">y</span><span class="o">.</span><span class="n">title</span><span class="p">(),</span> 
<span class="c1">#              text=&#39;This is the title&#39;,</span>
             <span class="c1">#title=f&#39;{y.title()} vs {x.title()}&#39;,</span>
            <span class="n">theme</span><span class="o">=</span><span class="n">theme</span><span class="p">,</span> <span class="n">colorscale</span><span class="o">=</span><span class="n">colorscale</span><span class="p">)</span>
</pre></div>

    </div>
</div>
</div>

  </div>
<div class="cell border-box-sizing text_cell rendered"><div class="inner_cell">
<div class="text_cell_render border-box-sizing rendered_html">
<h1 id="KEGG-Annotations">KEGG Annotations<a class="anchor-link" href="#KEGG-Annotations">&#182;</a></h1>
</div>
</div>
</div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">annotations</span> <span class="o">=</span> <span class="n">read_csv</span><span class="p">(</span><span class="s2">&quot;annotations/MetagenomicAssemblyAnnotations.txt&quot;</span><span class="p">,</span><span class="n">sep</span><span class="o">=</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
<span class="c1">#annotations = read_csv(&quot;annotations/Test.txt&quot;,sep=&#39;\t&#39;)</span>

<span class="n">annotations</span> <span class="o">=</span> <span class="n">annotations</span><span class="o">.</span><span class="n">sort_values</span><span class="p">(</span><span class="s1">&#39;evalue&#39;</span><span class="p">,</span><span class="n">ascending</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span><span class="o">.</span><span class="n">groupby</span><span class="p">(</span><span class="s1">&#39;qseqid&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">head</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span>
<span class="n">annotations</span><span class="o">.</span><span class="n">set_index</span><span class="p">(</span><span class="s2">&quot;qseqid&quot;</span><span class="p">,</span><span class="n">inplace</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="n">annotations</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
<span class="n">prin</span><span class="p">(</span><span class="n">annotations</span><span class="o">=</span><span class="n">annotations</span><span class="p">[</span><span class="n">annotations</span><span class="p">[</span><span class="s2">&quot;evalue&quot;</span><span class="p">]</span><span class="o">&lt;=</span><span class="mf">1.0e-5</span><span class="p">])</span>
<span class="nb">print</span><span class="p">(</span><span class="n">annotations</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
<span class="n">annotations</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span><span class="s2">&quot;annotations/MetagenomicAssemblyAnnotations_tophit.tsv&quot;</span><span class="p">,</span><span class="n">sep</span><span class="o">=</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
<span class="n">annotations</span><span class="p">[</span><span class="n">annotations</span><span class="o">.</span><span class="n">index</span><span class="o">==</span><span class="s1">&#39;k127_13265132&#39;</span><span class="p">]</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">annotations</span> <span class="o">=</span> <span class="n">read_csv</span><span class="p">(</span><span class="s2">&quot;annotations/MetagenomicAssemblyAnnotations_tophit.tsv&quot;</span><span class="p">,</span><span class="n">sep</span><span class="o">=</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
<span class="n">annotations</span><span class="o">.</span><span class="n">set_index</span><span class="p">(</span><span class="s2">&quot;qseqid&quot;</span><span class="p">,</span><span class="n">inplace</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="n">annotations</span><span class="o">.</span><span class="n">sort_values</span><span class="p">(</span><span class="s2">&quot;sseqid&quot;</span><span class="p">,</span><span class="n">inplace</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="n">annotations</span><span class="o">.</span><span class="n">head</span><span class="p">()</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">ko_map</span> <span class="o">=</span> <span class="n">read_csv</span><span class="p">(</span><span class="s2">&quot;annotations/ko/prokaryotes.dat&quot;</span><span class="p">,</span><span class="n">sep</span><span class="o">=</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
<span class="c1"># ko_map.set_index(&quot;GENE&quot;)</span>
<span class="nb">print</span><span class="p">(</span><span class="n">ko_map</span><span class="o">.</span><span class="n">shape</span><span class="p">)</span>
<span class="n">ko_map</span><span class="o">.</span><span class="n">head</span><span class="p">()</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="nb">len</span><span class="p">(</span><span class="n">ko_map</span><span class="o">.</span><span class="n">GENE</span><span class="o">.</span><span class="n">unique</span><span class="p">()),</span><span class="n">ko_map</span><span class="o">.</span><span class="n">shape</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">ko_map</span><span class="p">[</span><span class="n">ko_map</span><span class="p">[</span><span class="s2">&quot;GENE&quot;</span><span class="p">]</span><span class="o">==</span><span class="s2">&quot;&quot;</span><span class="p">]</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="kn">from</span> <span class="nn">pandas</span> <span class="k">import</span> <span class="n">merge</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">annotations</span><span class="o">.</span><span class="n">shape</span><span class="p">,</span><span class="n">genesW_KO</span><span class="o">.</span><span class="n">shape</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="nb">len</span><span class="p">(</span><span class="n">annotations</span><span class="o">.</span><span class="n">sseqid</span><span class="o">.</span><span class="n">unique</span><span class="p">())</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">done</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">genesW_KO</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="n">annotations</span><span class="o">.</span><span class="n">sseqid</span><span class="o">.</span><span class="n">unique</span><span class="p">())</span><span class="o">.</span><span class="n">intersection</span><span class="p">(</span><span class="n">ko_map</span><span class="o">.</span><span class="n">GENE</span><span class="p">)</span>
<span class="nb">len</span><span class="p">(</span><span class="n">genesW_KO</span><span class="p">)</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">genesW_KO</span> <span class="o">=</span> <span class="n">merge</span><span class="p">(</span><span class="n">annotations</span><span class="p">,</span> <span class="n">ko_map</span><span class="p">,</span> <span class="n">how</span><span class="o">=</span><span class="s1">&#39;inner&#39;</span><span class="p">,</span><span class="n">left_on</span><span class="o">=</span><span class="s2">&quot;sseqid&quot;</span><span class="p">,</span><span class="n">right_on</span><span class="o">=</span><span class="s2">&quot;GENE&quot;</span><span class="p">)</span>
<span class="n">genesW_KO</span><span class="o">.</span><span class="n">tail</span><span class="p">()</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">done</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">annotation_hierarchy</span> <span class="o">=</span> <span class="n">read_csv</span><span class="p">(</span><span class="s2">&quot;annotations/KeggAnnotationTable_filtered.tsv&quot;</span><span class="p">,</span><span class="n">sep</span><span class="o">=</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
<span class="n">annotation_hierarchy</span><span class="p">[</span><span class="s2">&quot;EC#&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="s2">&quot;&quot;</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">annotation_hierarchy</span><span class="o">.</span><span class="n">index</span><span class="p">:</span>
    <span class="n">function</span> <span class="o">=</span> <span class="n">annotation_hierarchy</span><span class="o">.</span><span class="n">at</span><span class="p">[</span><span class="n">i</span><span class="p">,</span><span class="s1">&#39;function&#39;</span><span class="p">]</span>
    <span class="n">ecNumIndex</span> <span class="o">=</span> <span class="n">function</span><span class="o">.</span><span class="n">rfind</span><span class="p">(</span><span class="s2">&quot; [EC&quot;</span><span class="p">)</span>
    <span class="k">if</span> <span class="n">ecNumIndex</span> <span class="o">!=</span> <span class="o">-</span><span class="mi">1</span><span class="p">:</span>
        <span class="n">annotation_hierarchy</span><span class="o">.</span><span class="n">at</span><span class="p">[</span><span class="n">i</span><span class="p">,</span><span class="s1">&#39;EC#&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">function</span><span class="p">[</span><span class="n">ecNumIndex</span><span class="o">+</span><span class="mi">2</span><span class="p">:</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
        <span class="n">annotation_hierarchy</span><span class="o">.</span><span class="n">at</span><span class="p">[</span><span class="n">i</span><span class="p">,</span><span class="s1">&#39;function&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">function</span><span class="p">[:</span><span class="n">ecNumIndex</span><span class="p">]</span>
<span class="n">annotation_hierarchy</span><span class="o">.</span><span class="n">head</span><span class="p">(</span><span class="mi">5</span><span class="p">)</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="nb">len</span><span class="p">(</span><span class="n">annotation_hierarchy</span><span class="o">.</span><span class="n">level3</span><span class="o">.</span><span class="n">unique</span><span class="p">())</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="k">for</span> <span class="n">function</span> <span class="ow">in</span> <span class="n">annotation_hierarchy</span><span class="o">.</span><span class="n">level3</span><span class="o">.</span><span class="n">unique</span><span class="p">():</span>
    
    <span class="nb">print</span><span class="p">(</span><span class="n">function</span><span class="p">)</span>
    <span class="k">break</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="nb">len</span><span class="p">(</span><span class="n">annotation_hierarchy</span><span class="o">.</span><span class="n">id</span><span class="o">.</span><span class="n">unique</span><span class="p">()),</span><span class="nb">len</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">ko_map</span><span class="o">.</span><span class="n">KO_NUM</span><span class="o">.</span><span class="n">unique</span><span class="p">())),</span><span class="nb">len</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">ko_map</span><span class="o">.</span><span class="n">KO_NUM</span><span class="o">.</span><span class="n">unique</span><span class="p">())</span><span class="o">.</span><span class="n">intersection</span><span class="p">(</span><span class="n">annotation_hierarchy</span><span class="o">.</span><span class="n">id</span><span class="p">))</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
<span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">merge</span><span class="p">(</span><span class="n">annotation_hierarchy</span><span class="p">,</span> <span class="n">ko_map</span><span class="p">,</span> <span class="n">left_on</span><span class="o">=</span><span class="s1">&#39;id&#39;</span><span class="p">,</span><span class="n">right_on</span><span class="o">=</span><span class="s1">&#39;KO_NUM&#39;</span><span class="p">,</span> <span class="n">how</span><span class="o">=</span><span class="s1">&#39;left&#39;</span><span class="p">)</span>
<span class="n">df</span><span class="o">.</span><span class="n">head</span><span class="p">()</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">uniqGenes</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="n">df</span><span class="p">[</span><span class="s2">&quot;GENE&quot;</span><span class="p">]</span><span class="o">.</span><span class="n">unique</span><span class="p">())</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">foundGenes</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
<span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">open</span><span class="p">(</span><span class="s2">&quot;annotations/UniqFoundGenes.txt&quot;</span><span class="p">):</span> <span class="n">foundGenes</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">())</span>
<span class="nb">len</span><span class="p">(</span><span class="n">foundGenes</span><span class="p">)</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="nb">len</span><span class="p">(</span><span class="n">foundGenes</span><span class="o">.</span><span class="n">difference</span><span class="p">(</span><span class="n">uniqGenes</span><span class="p">))</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">ko_genes</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="n">ko_map</span><span class="p">[</span><span class="s1">&#39;GENE&#39;</span><span class="p">])</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">koToContigMap</span> <span class="o">=</span> <span class="p">{}</span>
<span class="n">contigToKO</span> <span class="o">=</span> <span class="p">{}</span>
<span class="n">missing</span> <span class="o">=</span> <span class="mi">0</span>
<span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">open</span><span class="p">(</span><span class="s2">&quot;annotations/ContigsW_Annotations.txt&quot;</span><span class="p">):</span>
    <span class="n">contig</span><span class="p">,</span><span class="n">gene</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
    <span class="k">if</span> <span class="n">gene</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">ko_genes</span><span class="p">:</span><span class="n">missing</span> <span class="o">+=</span> <span class="mi">1</span><span class="p">;</span> <span class="k">continue</span>
    <span class="n">subKO_Map</span> <span class="o">=</span> <span class="n">ko_map</span><span class="p">[</span><span class="n">ko_map</span><span class="p">[</span><span class="s2">&quot;GENE&quot;</span><span class="p">]</span> <span class="o">==</span> <span class="n">gene</span><span class="p">]</span>
    <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">subKO_Map</span><span class="o">.</span><span class="n">iterrows</span><span class="p">():</span>
        <span class="n">ko</span> <span class="o">=</span> <span class="n">row</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="s1">&#39;KO_NUM&#39;</span><span class="p">]</span>
        <span class="k">try</span><span class="p">:</span> <span class="n">koToContigMap</span><span class="p">[</span><span class="n">ko</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">contig</span><span class="p">)</span>
        <span class="k">except</span><span class="p">:</span> <span class="n">koToContigMap</span><span class="p">[</span><span class="n">ko</span><span class="p">]</span> <span class="o">=</span><span class="nb">set</span><span class="p">([</span><span class="n">contig</span><span class="p">])</span>
        <span class="k">try</span><span class="p">:</span> <span class="n">contigToKO</span><span class="p">[</span><span class="n">contig</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">ko</span><span class="p">)</span>
        <span class="k">except</span><span class="p">:</span> <span class="n">contigToKO</span><span class="p">[</span><span class="n">contig</span><span class="p">]</span> <span class="o">=</span><span class="nb">set</span><span class="p">([</span><span class="n">ko</span><span class="p">])</span>
        
<span class="kn">from</span> <span class="nn">pickle</span> <span class="k">import</span> <span class="n">dump</span>
<span class="n">dump</span><span class="p">(</span><span class="n">koToContigMap</span><span class="p">,</span><span class="nb">open</span><span class="p">(</span><span class="s1">&#39;pickles/KO_ToContigMap.p&#39;</span><span class="p">,</span><span class="s1">&#39;wb&#39;</span><span class="p">))</span>
<span class="n">dump</span><span class="p">(</span><span class="n">koToContigMap</span><span class="p">,</span><span class="nb">open</span><span class="p">(</span><span class="s1">&#39;pickles/ContigToKO.p&#39;</span><span class="p">,</span><span class="s1">&#39;wb&#39;</span><span class="p">))</span>
<span class="nb">len</span><span class="p">(</span><span class="n">contigToKO</span><span class="p">),</span><span class="n">missing</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">metagenomeAnnotations</span> <span class="o">=</span> <span class="n">read_csv</span><span class="p">(</span><span class="s2">&quot;annotations/ContigsW_Annotations.txt&quot;</span><span class="p">,</span><span class="n">sep</span><span class="o">=</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
</pre></div>

    </div>
</div>
</div>

  </div>
<div class="cell border-box-sizing text_cell rendered"><div class="inner_cell">
<div class="text_cell_render border-box-sizing rendered_html">
<h3 id="Create-the-level-3-table">Create the level 3 table<a class="anchor-link" href="#Create-the-level-3-table">&#182;</a></h3>
</div>
</div>
</div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">genes</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
<span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">open</span><span class="p">(</span><span class="s2">&quot;annotations/UniqFoundGenes.txt&quot;</span><span class="p">):</span>
    <span class="n">genes</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">())</span>
<span class="nb">len</span><span class="p">(</span><span class="n">genes</span><span class="p">),</span><span class="nb">len</span><span class="p">(</span><span class="n">genes</span><span class="o">.</span><span class="n">difference</span><span class="p">(</span><span class="n">ko_map</span><span class="o">.</span><span class="n">GENE</span><span class="p">))</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">df</span><span class="p">[</span><span class="n">df</span><span class="p">[</span><span class="s2">&quot;level3&quot;</span><span class="p">]</span><span class="o">==</span><span class="s2">&quot;Glycolysis / Gluconeogenesis [PATH:ko00010]&quot;</span><span class="p">]</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
<span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">merge</span><span class="p">(</span><span class="n">annotation_hierarchy</span><span class="p">,</span> <span class="n">ko_map</span><span class="p">,</span> <span class="n">left_on</span><span class="o">=</span><span class="s1">&#39;function&#39;</span><span class="p">,</span><span class="n">right_on</span><span class="o">=</span><span class="s1">&#39;GENE&#39;</span><span class="p">,</span> <span class="n">how</span><span class="o">=</span><span class="s1">&#39;left&#39;</span><span class="p">)</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">df</span> <span class="o">=</span> <span class="n">read_csv</span><span class="p">(</span><span class="s2">&quot;annotations/ContigsW_Annotations.txt&quot;</span><span class="p">,</span><span class="n">sep</span><span class="o">=</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>

<span class="n">df</span><span class="o">.</span><span class="n">head</span><span class="p">(),</span> <span class="n">df</span><span class="o">.</span><span class="n">shape</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">ko_dict</span> <span class="o">=</span> <span class="p">{}</span>
<span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">ko_map</span><span class="o">.</span><span class="n">iterrows</span><span class="p">():</span>
    <span class="k">if</span> <span class="n">row</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">values</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="ow">in</span> <span class="n">ko_dict</span><span class="p">:</span>
        <span class="nb">print</span><span class="p">(</span><span class="n">row</span><span class="p">)</span>
        <span class="nb">print</span><span class="p">()</span>
        <span class="nb">print</span><span class="p">(</span><span class="n">ko_dict</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">values</span><span class="p">[</span><span class="mi">1</span><span class="p">]])</span>
        <span class="k">break</span>
    <span class="n">ko_dict</span><span class="p">[</span><span class="n">row</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">values</span><span class="p">[</span><span class="mi">1</span><span class="p">]]</span><span class="o">=</span><span class="n">row</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">values</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="kn">from</span> <span class="nn">collections</span> <span class="k">import</span> <span class="n">Counter</span>
<span class="n">annos</span> <span class="o">=</span> <span class="n">Annotation</span><span class="p">()</span>
<span class="n">missing</span> <span class="o">=</span> <span class="n">Counter</span><span class="p">()</span>
<span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="s2">&quot;annotations/MetagenomicAssemblyAnnotations_filtered_90PID.txt&quot;</span><span class="p">,</span><span class="s2">&quot;r&quot;</span><span class="p">)</span> <span class="k">as</span> <span class="n">fh</span><span class="p">:</span>
    <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">line</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">fh</span><span class="p">):</span>
        <span class="k">if</span> <span class="n">i</span><span class="o">%</span><span class="k">500000</span>==0:print(i,end=&#39; &#39;)
        <span class="n">rec</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">)</span>
        <span class="n">contigID</span><span class="p">,</span> <span class="n">geneID</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span><span class="n">rec</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
        <span class="n">val</span> <span class="o">=</span> <span class="n">ko_map</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="n">ko_map</span><span class="p">[</span><span class="s2">&quot;Gene&quot;</span><span class="p">]</span> <span class="o">==</span> <span class="n">geneID</span><span class="p">,[</span><span class="s1">&#39;KoNum&#39;</span><span class="p">]]</span>
        <span class="k">try</span><span class="p">:</span><span class="n">koNum</span> <span class="o">=</span> <span class="n">val</span><span class="o">.</span><span class="n">values</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span>
        <span class="k">except</span><span class="p">:</span> <span class="n">missing</span><span class="p">[</span><span class="n">geneID</span><span class="p">]</span> <span class="o">+=</span> <span class="mi">1</span>
        <span class="n">annos</span><span class="p">[</span><span class="n">contigID</span><span class="p">]</span> <span class="o">=</span> <span class="n">koNum</span>
<span class="n">dump</span><span class="p">(</span><span class="n">annos</span><span class="p">,</span><span class="nb">open</span><span class="p">(</span><span class="s2">&quot;pickles/ContigAnnotationMap.p&quot;</span><span class="p">,</span><span class="s2">&quot;wb&quot;</span><span class="p">))</span>
<span class="n">dump</span><span class="p">(</span><span class="n">missing</span><span class="p">,</span><span class="nb">open</span><span class="p">(</span><span class="s2">&quot;pickles/NotInKO_Map.p&quot;</span><span class="p">,</span><span class="s2">&quot;wb&quot;</span><span class="p">))</span>
<span class="nb">len</span><span class="p">(</span><span class="n">missing</span><span class="p">)</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span> 
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span> 
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="kn">from</span> <span class="nn">random</span> <span class="k">import</span> <span class="n">randint</span>
<span class="k">class</span> <span class="nc">Annotation</span><span class="p">:</span>
    <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
        <span class="bp">self</span><span class="o">.</span><span class="n">contigs</span> <span class="o">=</span> <span class="p">{}</span> <span class="c1"># ContigsName -&gt; set of related Annotations</span>
        <span class="bp">self</span><span class="o">.</span><span class="n">annotations</span> <span class="o">=</span> <span class="p">{}</span> <span class="c1"># KO number -&gt; contigs with that KO</span>
    <span class="k">def</span> <span class="nf">__setitem__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">key</span><span class="p">,</span><span class="n">value</span><span class="p">):</span>
        <span class="k">try</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">contigs</span><span class="p">[</span><span class="n">key</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">value</span><span class="p">)</span>
        <span class="k">except</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">contigs</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="n">value</span><span class="p">]</span>
        <span class="k">try</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">annotations</span><span class="p">[</span><span class="n">value</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">key</span><span class="p">)</span>
        <span class="k">except</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">annotations</span><span class="p">[</span><span class="n">value</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="n">key</span><span class="p">]</span>
    <span class="k">def</span> <span class="nf">__getitem__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">key</span><span class="p">):</span> <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">contigs</span><span class="p">[</span><span class="n">key</span><span class="p">][</span><span class="n">randint</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">contigs</span><span class="p">[</span><span class="n">key</span><span class="p">]))]</span>
</pre></div>

    </div>
</div>
</div>

  </div>
<div class="cell border-box-sizing text_cell rendered"><div class="inner_cell">
<div class="text_cell_render border-box-sizing rendered_html">
<h1 id="Generating-the-annotation-fasta-files">Generating the annotation fasta files<a class="anchor-link" href="#Generating-the-annotation-fasta-files">&#182;</a></h1>
</div>
</div>
</div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="kn">from</span> <span class="nn">Bio.SeqIO</span> <span class="k">import</span> <span class="n">parse</span><span class="p">,</span> <span class="n">write</span>
<span class="kn">from</span> <span class="nn">Bio.SeqRecord</span> <span class="k">import</span> <span class="n">SeqRecord</span>
<span class="n">annotatedRegions</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="s2">&quot;assemblies/AnnotatedContigs.fa&quot;</span><span class="p">,</span><span class="s2">&quot;w&quot;</span><span class="p">)</span>
<span class="n">geneDescripts</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="s2">&quot;annotations/AnnotationDescripts.bed&quot;</span><span class="p">,</span><span class="s2">&quot;w&quot;</span><span class="p">)</span>
<span class="n">annotations</span> <span class="o">=</span> <span class="n">glob</span><span class="p">(</span><span class="s2">&quot;mags/final.contigs.*/*.gbk&quot;</span><span class="p">)</span>
<span class="n">seqs</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
<span class="n">hypoCounter</span> <span class="o">=</span> <span class="mi">0</span>
<span class="k">for</span> <span class="n">fname</span> <span class="ow">in</span> <span class="n">annotations</span><span class="p">:</span>
    <span class="k">for</span> <span class="n">rec</span> <span class="ow">in</span> <span class="n">parse</span><span class="p">(</span><span class="n">fname</span><span class="p">,</span><span class="s1">&#39;genbank&#39;</span><span class="p">):</span>
        <span class="k">for</span> <span class="n">feature</span> <span class="ow">in</span> <span class="n">rec</span><span class="o">.</span><span class="n">features</span><span class="p">:</span>
            <span class="k">try</span><span class="p">:</span>
                <span class="n">product</span> <span class="o">=</span> <span class="n">feature</span><span class="o">.</span><span class="n">qualifiers</span><span class="p">[</span><span class="s1">&#39;product&#39;</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span>
                <span class="c1">#if product == &quot;hypothetical protein&quot;:continue</span>
                <span class="c1">#subSeq = rec.seq[feature.location.start:feature.location.end]</span>
                <span class="n">hypoCounter</span> <span class="o">+=</span> <span class="nb">int</span><span class="p">(</span><span class="n">product</span> <span class="o">==</span> <span class="s2">&quot;hypothetical protein&quot;</span><span class="p">)</span>
                <span class="n">geneDescripts</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">&quot;</span><span class="si">%s</span><span class="se">\t</span><span class="si">%i</span><span class="se">\t</span><span class="si">%i</span><span class="se">\t</span><span class="si">%s</span><span class="se">\n</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">rec</span><span class="o">.</span><span class="n">id</span><span class="p">,</span><span class="n">feature</span><span class="o">.</span><span class="n">location</span><span class="o">.</span><span class="n">start</span><span class="p">,</span><span class="n">feature</span><span class="o">.</span><span class="n">location</span><span class="o">.</span><span class="n">end</span><span class="p">,</span><span class="n">product</span><span class="p">))</span>
                <span class="k">if</span> <span class="n">rec</span><span class="o">.</span><span class="n">id</span> <span class="ow">in</span> <span class="n">seqs</span><span class="p">:</span> <span class="k">continue</span>
                <span class="n">rec</span><span class="o">.</span><span class="n">seq</span> <span class="o">=</span> <span class="n">rec</span><span class="o">.</span><span class="n">seq</span><span class="o">.</span><span class="n">upper</span><span class="p">()</span>
                <span class="n">write</span><span class="p">(</span><span class="n">rec</span><span class="p">,</span><span class="n">annotatedRegions</span><span class="p">,</span><span class="s2">&quot;fasta&quot;</span><span class="p">)</span>
                <span class="n">seqs</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">rec</span><span class="o">.</span><span class="n">id</span><span class="p">)</span>
            <span class="k">except</span><span class="p">:</span><span class="k">pass</span>
<span class="n">annotatedRegions</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
<span class="n">geneDescripts</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
</pre></div>

    </div>
</div>
</div>

  </div>
<div class="cell border-box-sizing text_cell rendered"><div class="inner_cell">
<div class="text_cell_render border-box-sizing rendered_html">
<h2><a id="occon">Calculate Abundance and occupancy of contigs in samples</a></h2>
</div>
</div>
</div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="c1">#Individual Sample</span>
<span class="kn">from</span> <span class="nn">collections</span> <span class="k">import</span> <span class="n">Counter</span>
<span class="n">seqPresenceCounter</span><span class="p">,</span> <span class="n">seqMappedCounter</span> <span class="o">=</span> <span class="n">Counter</span><span class="p">(),</span> <span class="n">Counter</span><span class="p">()</span>
<span class="n">missingFiles</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
<span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">statFName</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">metadata</span><span class="o">.</span><span class="n">index</span><span class="p">):</span>
    <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;</span><span class="si">%i</span><span class="s2">. </span><span class="si">%s</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">i</span><span class="p">,</span><span class="n">statFName</span><span class="p">),</span><span class="n">end</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
    <span class="k">try</span><span class="p">:</span>
        <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="s2">&quot;mapping/metaG/stats/</span><span class="si">%s</span><span class="s2">.tsv&quot;</span> <span class="o">%</span> <span class="n">statFName</span><span class="p">)</span> <span class="k">as</span> <span class="n">fh</span><span class="p">:</span>
            <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">fh</span><span class="p">:</span>
                <span class="n">rec</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">()</span>
                <span class="n">seqMappedCounter</span><span class="p">[</span><span class="n">rec</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span> <span class="o">+=</span> <span class="nb">int</span><span class="p">(</span><span class="n">rec</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>
                <span class="n">seqPresenceCounter</span><span class="p">[</span><span class="n">rec</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span> <span class="o">+=</span> <span class="nb">int</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">rec</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span><span class="o">&gt;</span><span class="mi">0</span><span class="p">)</span>
        <span class="k">if</span> <span class="n">i</span> <span class="o">%</span> <span class="mi">3</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span><span class="nb">print</span><span class="p">()</span>
    <span class="k">except</span><span class="p">:</span>
        <span class="n">missingFiles</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="s2">&quot;mapping/metaG/stats/</span><span class="si">%s</span><span class="s2">.tsv&quot;</span> <span class="o">%</span> <span class="n">statFName</span><span class="p">)</span>
<span class="n">dump</span><span class="p">(</span><span class="n">seqPresenceCounter</span><span class="p">,</span><span class="nb">open</span><span class="p">(</span><span class="s2">&quot;pickles/seqPresenceCounter_genes.p&quot;</span><span class="p">,</span><span class="s2">&quot;wb&quot;</span><span class="p">))</span>
<span class="n">dump</span><span class="p">(</span><span class="n">seqMappedCounter</span><span class="p">,</span>  <span class="nb">open</span><span class="p">(</span><span class="s2">&quot;pickles/seqMappedCounter_genes.p&quot;</span><span class="p">,</span>  <span class="s2">&quot;wb&quot;</span><span class="p">))</span>  
<span class="n">seqPresenceDist</span> <span class="o">=</span> <span class="n">Series</span><span class="p">(</span><span class="n">load</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="s2">&quot;pickles/seqPresenceCounter_genes.p&quot;</span><span class="p">,</span><span class="s2">&quot;rb&quot;</span><span class="p">)))</span><span class="o">/</span><span class="mf">136.0</span>
<span class="n">seqPresenceDist</span><span class="o">.</span><span class="n">plot</span><span class="o">.</span><span class="n">hist</span><span class="p">();</span>

<span class="n">dump</span><span class="p">(</span><span class="n">missingFiles</span><span class="p">,</span><span class="nb">open</span><span class="p">(</span><span class="s2">&quot;pickles/missingFiles_genes.p&quot;</span><span class="p">,</span><span class="s2">&quot;wb&quot;</span><span class="p">))</span> 
<span class="nb">len</span><span class="p">(</span><span class="n">missingFiles</span><span class="p">)</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">seqPresenceCounter</span> <span class="o">=</span> <span class="n">load</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="s2">&quot;pickles/seqPresenceCounter_genes.p&quot;</span><span class="p">,</span><span class="s2">&quot;rb&quot;</span><span class="p">))</span>
<span class="n">smp</span> <span class="o">=</span> <span class="n">Series</span><span class="p">(</span><span class="n">seqPresenceCounter</span><span class="p">)</span>
<span class="n">totalReads</span> <span class="o">=</span> <span class="n">smp</span><span class="o">.</span><span class="n">sum</span><span class="p">()</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">10</span><span class="p">):</span>
    <span class="n">sub</span> <span class="o">=</span> <span class="n">smp</span><span class="p">[</span><span class="n">smp</span> <span class="o">&lt;=</span> <span class="n">i</span> <span class="p">]</span>
    <span class="n">subSum</span> <span class="o">=</span> <span class="n">sub</span><span class="o">.</span><span class="n">sum</span><span class="p">()</span>
    <span class="nb">print</span><span class="p">(</span><span class="n">i</span><span class="p">,</span><span class="nb">len</span><span class="p">(</span><span class="n">sub</span><span class="p">),</span><span class="s2">&quot;</span><span class="si">%.2f%%</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">sub</span><span class="p">)</span><span class="o">/</span><span class="nb">len</span><span class="p">(</span><span class="n">smp</span><span class="p">)</span><span class="o">*</span><span class="mi">100</span><span class="p">),</span><span class="n">comma</span><span class="p">(</span><span class="n">subSum</span><span class="p">),</span><span class="s2">&quot;</span><span class="si">%.2f%%</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="p">((</span><span class="n">subSum</span><span class="o">/</span><span class="n">totalReads</span><span class="p">)</span><span class="o">*</span><span class="mi">100</span><span class="p">))</span>
<span class="nb">print</span><span class="p">()</span>
</pre></div>

    </div>
</div>
</div>

  </div>
<div class="cell border-box-sizing text_cell rendered"><div class="inner_cell">
<div class="text_cell_render border-box-sizing rendered_html">
<h1 id="Remove-anything-that-is-in-less-than-5-samples">Remove anything that is in less than 5 samples<a class="anchor-link" href="#Remove-anything-that-is-in-less-than-5-samples">&#182;</a></h1>
</div>
</div>
</div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="nb">print</span><span class="p">(</span><span class="s2">&quot;Before Number of genes:&quot;</span><span class="p">,</span><span class="n">comma</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">smp</span><span class="p">)))</span>
<span class="n">keepers</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="n">smp</span><span class="p">[</span><span class="n">smp</span> <span class="o">&gt;=</span> <span class="mi">5</span><span class="p">]</span><span class="o">.</span><span class="n">index</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s2">&quot;After Number of genes:&quot;</span><span class="p">,</span><span class="n">comma</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">keepers</span><span class="p">)))</span>
</pre></div>

    </div>
</div>
</div>

  </div>
<div class="cell border-box-sizing text_cell rendered"><div class="inner_cell">
<div class="text_cell_render border-box-sizing rendered_html">
<h1 id="Read-the-single-copy-number-values">Read the single copy number values<a class="anchor-link" href="#Read-the-single-copy-number-values">&#182;</a></h1>
</div>
</div>
</div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">files</span> <span class="o">=</span> <span class="n">glob</span><span class="p">(</span><span class="s2">&quot;mapping/metaG/annotatedContigs/logs/singleCopyGeneCounts/*.txt&quot;</span><span class="p">)</span>
<span class="n">metadata</span><span class="p">[</span><span class="s2">&quot;SingleCopyCount&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="mf">0.0</span>
<span class="k">for</span> <span class="n">fname</span> <span class="ow">in</span> <span class="n">files</span><span class="p">:</span>
    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">fname</span><span class="p">)</span> <span class="k">as</span> <span class="n">fh</span><span class="p">:</span>
        <span class="n">lines</span> <span class="o">=</span> <span class="n">fh</span><span class="o">.</span><span class="n">readlines</span><span class="p">()[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
        <span class="n">sampleName</span> <span class="o">=</span> <span class="n">fname</span><span class="p">[</span><span class="n">fname</span><span class="o">.</span><span class="n">rfind</span><span class="p">(</span><span class="s1">&#39;/&#39;</span><span class="p">)</span><span class="o">+</span><span class="mi">1</span><span class="p">:</span><span class="o">-</span><span class="mi">4</span><span class="p">]</span>
        <span class="n">metadata</span><span class="o">.</span><span class="n">at</span><span class="p">[</span><span class="n">sampleName</span><span class="p">,</span><span class="s2">&quot;SingleCopyCount&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">lines</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">])</span>
<span class="n">metadata</span><span class="o">.</span><span class="n">head</span><span class="p">()</span>
</pre></div>

    </div>
</div>
</div>

  </div>
<div class="cell border-box-sizing text_cell rendered"><div class="inner_cell">
<div class="text_cell_render border-box-sizing rendered_html">
<h1 id="Read-the-count-numbers-and-normalize">Read the count numbers and normalize<a class="anchor-link" href="#Read-the-count-numbers-and-normalize">&#182;</a></h1>
</div>
</div>
</div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="kn">from</span> <span class="nn">Bio.SeqIO</span> <span class="k">import</span> <span class="n">parse</span>
<span class="n">readLens</span><span class="o">=</span><span class="p">{}</span>
<span class="k">for</span> <span class="n">rec</span> <span class="ow">in</span> <span class="n">parse</span><span class="p">(</span><span class="s2">&quot;assemblies/AnnotatedContigs.fa&quot;</span><span class="p">,</span><span class="s2">&quot;fasta&quot;</span><span class="p">):</span> <span class="n">readLens</span><span class="p">[</span><span class="n">rec</span><span class="o">.</span><span class="n">id</span><span class="p">]</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">rec</span><span class="o">.</span><span class="n">seq</span><span class="p">)</span><span class="o">/</span><span class="mi">1000</span>
<span class="c1">#RPKG = (reads mapped to gene)/(gene length in kb)/(genome equivalents)</span>
<span class="nb">print</span><span class="p">(</span><span class="s2">&quot;Number of reads: </span><span class="si">%s</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">comma</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">readLens</span><span class="p">))))</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">readMap</span> <span class="o">=</span> <span class="p">{}</span>
<span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">open</span><span class="p">(</span><span class="s2">&quot;mapping/metaG/stats/G5R1_NF_09MAY2016_LD1.tsv&quot;</span><span class="p">):</span>
    <span class="n">rec</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">()</span>
    <span class="k">if</span> <span class="n">rec</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">keepers</span><span class="p">:</span><span class="k">continue</span>
    <span class="n">readName</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="mi">0</span><span class="p">][:</span><span class="n">rec</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">rfind</span><span class="p">(</span><span class="s2">&quot;_&quot;</span><span class="p">)]</span>
    <span class="n">readName</span> <span class="o">=</span> <span class="n">readName</span><span class="p">[:</span><span class="n">readName</span><span class="o">.</span><span class="n">rfind</span><span class="p">(</span><span class="s2">&quot;_&quot;</span><span class="p">)]</span>
    <span class="n">readMap</span><span class="p">[</span><span class="n">rec</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span> <span class="o">=</span> <span class="n">readName</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">allCounts</span><span class="p">,</span><span class="n">counter</span> <span class="o">=</span> <span class="p">{},</span><span class="mi">0</span>
<span class="k">for</span> <span class="n">sampleID</span> <span class="ow">in</span> <span class="n">metadata</span><span class="o">.</span><span class="n">index</span><span class="p">:</span>
    <span class="n">counter</span> <span class="o">+=</span> <span class="mi">1</span>
    <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;</span><span class="si">%i</span><span class="s2">. </span><span class="si">%s</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">counter</span><span class="p">,</span><span class="n">sampleID</span><span class="p">),</span><span class="n">end</span><span class="o">=</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
    <span class="n">allCounts</span><span class="p">[</span><span class="n">sampleID</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
    <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">open</span><span class="p">(</span><span class="s2">&quot;mapping/metaG/stats/</span><span class="si">%s</span><span class="s2">.tsv&quot;</span> <span class="o">%</span> <span class="n">sampleID</span><span class="p">):</span>
        <span class="n">rec</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">()</span>
        <span class="k">if</span> <span class="n">rec</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">keepers</span><span class="p">:</span><span class="k">continue</span>
        <span class="n">allCounts</span><span class="p">[</span><span class="n">sampleID</span><span class="p">][</span><span class="n">rec</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">rec</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span><span class="o">/</span><span class="n">readLens</span><span class="p">[</span><span class="n">readMap</span><span class="p">[</span><span class="n">rec</span><span class="p">[</span><span class="mi">0</span><span class="p">]]]</span><span class="o">/</span><span class="n">metadata</span><span class="o">.</span><span class="n">at</span><span class="p">[</span><span class="n">sampleID</span><span class="p">,</span><span class="s2">&quot;SingleCopyCount&quot;</span><span class="p">]</span>
    <span class="k">if</span> <span class="n">counter</span> <span class="o">%</span> <span class="mi">3</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span> <span class="nb">print</span><span class="p">()</span>
<span class="n">allCounts</span> <span class="o">=</span> <span class="n">DataFrame</span><span class="p">(</span><span class="n">allCounts</span><span class="p">)</span> 
<span class="n">dump</span><span class="p">(</span><span class="n">allCounts</span><span class="p">,</span><span class="nb">open</span><span class="p">(</span><span class="s2">&quot;pickles/allCounts_genes.p&quot;</span><span class="p">,</span><span class="s2">&quot;wb&quot;</span><span class="p">))</span>  
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">allCounts</span><span class="o">.</span><span class="n">head</span><span class="p">()</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">xs</span><span class="p">,</span> <span class="n">ys</span> <span class="o">=</span> <span class="p">[],[]</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span><span class="mi">101</span><span class="p">):</span>
    <span class="n">xs</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">i</span><span class="p">)</span>
    <span class="n">ys</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">seqPresenceDist</span><span class="p">[</span><span class="n">seqPresenceDist</span> <span class="o">&gt;=</span> <span class="n">i</span><span class="o">/</span><span class="mf">100.0</span><span class="p">]))</span>
<span class="n">plt</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">xs</span><span class="p">,</span><span class="n">ys</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">xlabel</span><span class="p">(</span><span class="s1">&#39;Percent of samples&#39;</span><span class="p">,</span><span class="n">fontsize</span><span class="o">=</span><span class="mi">14</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">ylabel</span><span class="p">(</span><span class="s1">&#39;Contigs with &gt;= 1 read&#39;</span><span class="p">,</span><span class="n">fontsize</span><span class="o">=</span><span class="mi">14</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">savefig</span><span class="p">(</span><span class="s2">&quot;figures/GeneAbundance.png&quot;</span><span class="p">,</span><span class="n">bbox_inches</span><span class="o">=</span><span class="s1">&#39;tight&#39;</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">show</span><span class="p">()</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">seqPresenceCounter</span> <span class="o">=</span> <span class="n">Series</span><span class="p">(</span><span class="n">load</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="s2">&quot;pickles/seqPresenceCounter_genes.p&quot;</span><span class="p">,</span><span class="s2">&quot;rb&quot;</span><span class="p">)))</span>
<span class="n">seqMappedCounter</span> <span class="o">=</span> <span class="n">Series</span><span class="p">(</span><span class="n">load</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="s2">&quot;pickles/seqMappedCounter_genes.p&quot;</span><span class="p">,</span><span class="s2">&quot;rb&quot;</span><span class="p">)))</span>
<span class="n">seqMappedCounter</span><span class="o">.</span><span class="n">describe</span><span class="p">()</span>
<span class="n">seqPresenceCounter</span><span class="o">.</span><span class="n">describe</span><span class="p">()</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">allCounts</span> <span class="o">=</span> <span class="n">load</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="s2">&quot;pickles/allCounts_genes.p&quot;</span><span class="p">,</span><span class="s2">&quot;rb&quot;</span><span class="p">))</span>
<span class="c1"># allCounts[&quot;Average&quot;] = allCounts.sum(axis=1)/float(len(allCounts.columns))</span>
<span class="c1"># allCounts[&quot;Average&quot;].head()</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">allCounts</span><span class="o">.</span><span class="n">head</span><span class="p">()</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="nb">print</span><span class="p">(</span><span class="s2">&quot;Before Filtering:&quot;</span><span class="p">,</span><span class="nb">len</span><span class="p">(</span><span class="n">allCounts</span><span class="p">))</span>
<span class="n">allCounts</span> <span class="o">=</span> <span class="n">allCounts</span><span class="p">[</span><span class="n">allCounts</span><span class="p">[</span><span class="s2">&quot;Average&quot;</span><span class="p">]</span><span class="o">&gt;</span><span class="mi">1</span><span class="p">]</span>
<span class="n">xs</span><span class="p">,</span><span class="n">ys</span><span class="o">=</span><span class="p">[],[]</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span><span class="mi">30</span><span class="p">):</span>
    <span class="n">xs</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">i</span><span class="p">)</span>
    <span class="n">ys</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">allCounts</span><span class="p">[</span><span class="n">allCounts</span><span class="p">[</span><span class="s2">&quot;Average&quot;</span><span class="p">]</span> <span class="o">&gt;</span> <span class="n">i</span><span class="p">]))</span>
    <span class="n">xs</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">i</span><span class="o">+.</span><span class="mi">5</span><span class="p">)</span>
    <span class="n">ys</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">allCounts</span><span class="p">[</span><span class="n">allCounts</span><span class="p">[</span><span class="s2">&quot;Average&quot;</span><span class="p">]</span> <span class="o">&gt;</span> <span class="n">i</span><span class="o">+.</span><span class="mi">5</span><span class="p">]))</span>
    
<span class="n">allCounts</span><span class="o">.</span><span class="n">drop</span><span class="p">(</span><span class="s2">&quot;Average&quot;</span><span class="p">,</span><span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span><span class="n">inplace</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s2">&quot;After Filtering:&quot;</span><span class="p">,</span><span class="nb">len</span><span class="p">(</span><span class="n">allCounts</span><span class="p">))</span>
<span class="c1">#allCounts = allCounts.transpose()</span>
<span class="c1">#allCounts= DataFrame(allCounts,index=allCounts.index)</span>
<span class="n">dump</span><span class="p">(</span><span class="n">allCounts</span><span class="p">,</span><span class="nb">open</span><span class="p">(</span><span class="s2">&quot;pickles/allCountsFiltered_genes.p&quot;</span><span class="p">,</span><span class="s2">&quot;wb&quot;</span><span class="p">))</span> 
<span class="n">plt</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">xs</span><span class="p">,</span><span class="n">ys</span><span class="p">)</span>
<span class="c1"># plt.xlabel(&#39;Percent of samples&#39;,fontsize=14)</span>
<span class="c1"># plt.ylabel(&#39;Read Count&#39;,fontsize=14)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">savefig</span><span class="p">(</span><span class="s2">&quot;figures/GeneAvgCount.png&quot;</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">show</span><span class="p">()</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">sortedmeta</span> <span class="o">=</span> <span class="n">metadata</span><span class="p">[[</span><span class="s2">&quot;sampling_date&quot;</span><span class="p">,</span><span class="s2">&quot;Date&quot;</span><span class="p">,</span><span class="s2">&quot;type&quot;</span><span class="p">,</span><span class="s2">&quot;nucleic_acid_name&quot;</span><span class="p">,</span><span class="s2">&quot;treatment&quot;</span><span class="p">]]</span>
<span class="n">sortedmeta</span> <span class="o">=</span> <span class="n">sortedmeta</span><span class="o">.</span><span class="n">sort_values</span><span class="p">(</span><span class="n">by</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;type&quot;</span><span class="p">,</span><span class="s2">&quot;Date&quot;</span><span class="p">])</span>
<span class="n">counter</span> <span class="o">=</span> <span class="mi">0</span>
<span class="n">sampleOrder</span> <span class="o">=</span> <span class="p">{}</span>  
<span class="k">for</span> <span class="nb">id</span> <span class="ow">in</span> <span class="n">sortedmeta</span><span class="o">.</span><span class="n">nucleic_acid_name</span><span class="p">:</span>
    <span class="n">counter</span><span class="o">+=</span><span class="mi">1</span>
    <span class="n">sampleOrder</span><span class="p">[</span><span class="nb">id</span><span class="p">]</span> <span class="o">=</span> <span class="n">counter</span>

<span class="n">allCounts</span> <span class="o">=</span> <span class="n">DataFrame</span><span class="p">(</span><span class="n">allCounts</span><span class="p">)</span><span class="o">.</span><span class="n">transpose</span><span class="p">()</span>
<span class="n">allCounts</span><span class="p">[</span><span class="s1">&#39;Rank&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">allCounts</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">to_series</span><span class="p">()</span><span class="o">.</span><span class="n">map</span><span class="p">(</span><span class="n">sampleOrder</span><span class="p">)</span>
<span class="n">allCounts</span><span class="o">.</span><span class="n">sort_values</span><span class="p">(</span><span class="s1">&#39;Rank&#39;</span><span class="p">,</span><span class="n">inplace</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
<span class="n">allCounts</span><span class="o">.</span><span class="n">drop</span><span class="p">(</span><span class="s1">&#39;Rank&#39;</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="n">inplace</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
<span class="n">dump</span><span class="p">(</span><span class="n">allCounts</span><span class="p">,</span><span class="nb">open</span><span class="p">(</span><span class="s2">&quot;pickles/allCountsFilteredSorted_genes.p&quot;</span><span class="p">,</span><span class="s2">&quot;wb&quot;</span><span class="p">))</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">allCounts</span> <span class="o">=</span> <span class="n">load</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="s2">&quot;pickles/allCountsFilteredSorted_genes.p&quot;</span><span class="p">,</span><span class="s2">&quot;rb&quot;</span><span class="p">))</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="c1">#allCounts = DataFrame(combined_abundance)</span>
<span class="n">seed</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">RandomState</span><span class="p">(</span><span class="n">seed</span><span class="o">=</span><span class="mi">3</span><span class="p">)</span>
<span class="n">allCounts_matrix</span> <span class="o">=</span> <span class="n">allCounts</span><span class="o">.</span><span class="n">as_matrix</span><span class="p">()</span>
<span class="nb">print</span><span class="p">(</span><span class="s2">&quot;Calculating Distance&quot;</span><span class="p">)</span>
<span class="n">similarities</span> <span class="o">=</span> <span class="n">euclidean_distances</span><span class="p">(</span><span class="n">allCounts_matrix</span><span class="p">)</span>

<span class="n">nsamples</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">allCounts</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s2">&quot;Running NMDS with </span><span class="si">%i</span><span class="s2"> samples&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">nsamples</span><span class="p">))</span>
<span class="n">mds</span> <span class="o">=</span> <span class="n">manifold</span><span class="o">.</span><span class="n">MDS</span><span class="p">(</span><span class="n">n_components</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span> <span class="n">max_iter</span><span class="o">=</span><span class="mi">3000</span><span class="p">,</span> <span class="n">eps</span><span class="o">=</span><span class="mf">1e-9</span><span class="p">,</span> <span class="n">random_state</span><span class="o">=</span><span class="n">seed</span><span class="p">,</span> <span class="n">dissimilarity</span><span class="o">=</span><span class="s2">&quot;precomputed&quot;</span><span class="p">,</span> <span class="n">n_jobs</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
<span class="n">pos</span> <span class="o">=</span> <span class="n">mds</span><span class="o">.</span><span class="n">fit</span><span class="p">(</span><span class="n">similarities</span><span class="p">)</span><span class="o">.</span><span class="n">embedding_</span>
<span class="n">nmds</span> <span class="o">=</span> <span class="n">manifold</span><span class="o">.</span><span class="n">MDS</span><span class="p">(</span><span class="n">n_components</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span> <span class="n">metric</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">max_iter</span><span class="o">=</span><span class="mi">3000</span><span class="p">,</span> <span class="n">eps</span><span class="o">=</span><span class="mf">1e-12</span><span class="p">,</span> <span class="n">dissimilarity</span><span class="o">=</span><span class="s2">&quot;precomputed&quot;</span><span class="p">,</span> <span class="n">random_state</span><span class="o">=</span><span class="n">seed</span><span class="p">,</span> <span class="n">n_jobs</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">n_init</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
<span class="n">npos</span> <span class="o">=</span> <span class="n">nmds</span><span class="o">.</span><span class="n">fit_transform</span><span class="p">(</span><span class="n">similarities</span><span class="p">,</span> <span class="n">init</span><span class="o">=</span><span class="n">pos</span><span class="p">)</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="kn">import</span> <span class="nn">matplotlib</span> <span class="k">as</span> <span class="nn">mpl</span>
<span class="n">fig</span> <span class="o">=</span> <span class="n">plt</span><span class="o">.</span><span class="n">figure</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span>
<span class="n">ax</span> <span class="o">=</span> <span class="n">plt</span><span class="o">.</span><span class="n">axes</span><span class="p">([</span><span class="mf">0.</span><span class="p">,</span> <span class="mf">0.</span><span class="p">,</span> <span class="mf">1.5</span><span class="p">,</span> <span class="mf">1.95</span><span class="p">])</span>
<span class="n">s</span> <span class="o">=</span> <span class="mi">100</span>
<span class="n">index</span> <span class="o">=</span> <span class="mi">0</span>
<span class="n">totalGroups</span> <span class="o">=</span> <span class="n">nsamples</span><span class="o">/</span><span class="mi">4</span>
<span class="n">l1s</span><span class="p">,</span> <span class="n">l2s</span> <span class="o">=</span> <span class="p">[],</span> <span class="p">[]</span>
<span class="n">dateColors</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">sample</span> <span class="ow">in</span> <span class="n">sortedmeta</span><span class="o">.</span><span class="n">index</span><span class="p">:</span>
<span class="c1">#     print(sample)</span>
    <span class="k">if</span> <span class="n">sortedmeta</span><span class="p">[</span><span class="n">sortedmeta</span><span class="o">.</span><span class="n">index</span> <span class="o">==</span> <span class="n">sample</span><span class="p">]</span><span class="o">.</span><span class="n">type</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s2">&quot;G5&quot;</span><span class="p">:</span> 
        <span class="n">species</span> <span class="o">=</span> <span class="s2">&quot;SG&quot;</span>
        <span class="k">if</span> <span class="n">sortedmeta</span><span class="p">[</span><span class="n">sortedmeta</span><span class="o">.</span><span class="n">index</span> <span class="o">==</span> <span class="n">sample</span><span class="p">]</span><span class="o">.</span><span class="n">treatment</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s2">&quot;nitrogen free&quot;</span><span class="p">:</span> 
            <span class="n">treatment</span> <span class="o">=</span> <span class="s2">&quot;NF&quot;</span>
            <span class="n">marker</span> <span class="o">=</span> <span class="s1">&#39;^&#39;</span>
        <span class="k">else</span><span class="p">:</span> 
            <span class="n">treatment</span> <span class="o">=</span> <span class="s2">&quot;Fert&quot;</span>
            <span class="n">marker</span><span class="o">=</span> <span class="s2">&quot;v&quot;</span>
    <span class="k">else</span><span class="p">:</span> 
        <span class="n">species</span> <span class="o">=</span> <span class="s2">&quot;MC&quot;</span><span class="p">;</span> 
        <span class="k">if</span> <span class="n">sortedmeta</span><span class="p">[</span><span class="n">sortedmeta</span><span class="o">.</span><span class="n">index</span> <span class="o">==</span> <span class="n">sample</span><span class="p">]</span><span class="o">.</span><span class="n">treatment</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s2">&quot;nitrogen free&quot;</span><span class="p">:</span> 
            <span class="n">treatment</span> <span class="o">=</span> <span class="s2">&quot;NF&quot;</span>
            <span class="n">marker</span> <span class="o">=</span> <span class="s1">&#39;p&#39;</span>
        <span class="k">else</span><span class="p">:</span> 
            <span class="n">treatment</span> <span class="o">=</span> <span class="s2">&quot;Fert&quot;</span>
            <span class="n">marker</span><span class="o">=</span> <span class="s2">&quot;s&quot;</span>
    <span class="n">lbl</span> <span class="o">=</span> <span class="s2">&quot;</span><span class="si">%s</span><span class="s2">_</span><span class="si">%s</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">species</span><span class="p">,</span><span class="n">treatment</span><span class="p">)</span>
    <span class="n">date</span><span class="o">=</span><span class="n">sortedmeta</span><span class="p">[</span><span class="n">sortedmeta</span><span class="o">.</span><span class="n">index</span> <span class="o">==</span> <span class="n">sample</span><span class="p">]</span><span class="o">.</span><span class="n">Date</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
    <span class="n">dateColors</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">scolor</span><span class="p">(</span><span class="n">index</span><span class="p">,</span><span class="mi">72</span><span class="p">,</span><span class="n">species</span> <span class="o">==</span> <span class="s2">&quot;SG&quot;</span><span class="p">))</span>
    <span class="n">plt</span><span class="o">.</span><span class="n">scatter</span><span class="p">(</span><span class="n">npos</span><span class="p">[</span><span class="n">index</span><span class="p">:</span><span class="n">index</span><span class="o">+</span><span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">],</span> <span class="n">npos</span><span class="p">[</span><span class="n">index</span><span class="p">:</span><span class="n">index</span><span class="o">+</span><span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">],</span> <span class="n">color</span><span class="o">=</span><span class="n">scolor</span><span class="p">(</span><span class="n">index</span><span class="p">,</span><span class="mi">72</span><span class="p">,</span><span class="n">species</span> <span class="o">==</span> <span class="s2">&quot;SG&quot;</span><span class="p">),</span> <span class="n">s</span><span class="o">=</span><span class="n">s</span><span class="p">,</span> <span class="n">lw</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span><span class="n">label</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span><span class="n">cmap</span><span class="o">=</span><span class="s1">&#39;viridis&#39;</span><span class="p">,</span><span class="n">marker</span><span class="o">=</span><span class="n">marker</span><span class="p">)</span>
    <span class="n">index</span> <span class="o">+=</span> <span class="mi">1</span>

<span class="k">for</span> <span class="n">crop</span><span class="p">,</span><span class="n">marker</span> <span class="ow">in</span> <span class="p">[[</span><span class="s1">&#39;Switchgrass Unfertilized&#39;</span><span class="p">,</span><span class="s1">&#39;^&#39;</span><span class="p">],[</span><span class="s1">&#39;Switchgrass Fertilized&#39;</span><span class="p">,</span><span class="s1">&#39;v&#39;</span><span class="p">],[</span><span class="s1">&#39;Miscanthus Unfertilized&#39;</span><span class="p">,</span><span class="s1">&#39;p&#39;</span><span class="p">],[</span><span class="s1">&#39;Miscanthus Fertilized&#39;</span><span class="p">,</span><span class="s1">&#39;s&#39;</span><span class="p">],]:</span>
    <span class="n">midval</span> <span class="o">=</span> <span class="mi">63</span><span class="o">/</span><span class="mi">2</span>
    <span class="k">if</span> <span class="s2">&quot;Switchgrass&quot;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">crop</span><span class="p">:</span> <span class="n">midval</span> <span class="o">=</span> <span class="mi">72</span> <span class="o">+</span> <span class="mi">72</span><span class="o">/</span><span class="mi">2</span>
    <span class="nb">print</span><span class="p">(</span><span class="n">crop</span><span class="p">,</span> <span class="n">scolor</span><span class="p">(</span><span class="n">midval</span><span class="p">,</span><span class="mi">72</span><span class="p">,</span> <span class="s2">&quot;SG&quot;</span> <span class="ow">in</span> <span class="n">crop</span><span class="p">))</span>
    <span class="n">plt</span><span class="o">.</span><span class="n">scatter</span><span class="p">([],</span> <span class="p">[],</span> <span class="n">c</span><span class="o">=</span><span class="n">scolor</span><span class="p">(</span><span class="n">midval</span><span class="p">,</span><span class="mi">72</span><span class="p">,</span> <span class="s2">&quot;Switchgrass&quot;</span> <span class="ow">in</span> <span class="n">crop</span><span class="p">),</span> <span class="n">label</span><span class="o">=</span><span class="n">crop</span><span class="p">,</span> <span class="n">marker</span><span class="o">=</span><span class="n">marker</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">legend</span><span class="p">(</span><span class="n">scatterpoints</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">frameon</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">labelspacing</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">title</span><span class="o">=</span><span class="s1">&#39;&#39;</span><span class="p">)</span>
<span class="c1">#handles, labels = ax.get_legend_handles_labels()</span>
<span class="c1"># plt.axis(aspect=&#39;equal&#39;)</span>
<span class="c1">#cmap = mpl.colors.ListedColormap(dateColors)</span>
<span class="c1">#cb1 = mpl.colorbar.ColorbarBase(ax, cmap=cmap, orientation=&#39;vertical&#39;)</span>
<span class="c1">#cb1.set_label(&#39;Some Units&#39;)</span>
<span class="c1">#psm = ax.pcolormesh(data, cmap=cmap, rasterized=True, vmin=-4, vmax=4)</span>
<span class="c1">#fig.colorbar(cmap, ax=ax)</span>
<span class="c1">#plt.colorbar(cmap, label=&#39;Time&#39;)</span>
<span class="c1"># plt.clim(3, 7)</span>
<span class="c1"># sort both labels and handles by labels</span>
<span class="c1"># labels, handles = zip(*sorted(zip(labels, handles), key=lambda t: t[0]))</span>
<span class="c1"># ax.legend(handles, labels)</span>
<span class="c1">#plt.legend(handles, labels,scatterpoints=1, loc=&#39;best&#39;, shadow=False)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">title</span><span class="p">(</span><span class="s2">&quot;Switchgrass and Miscanthus Fertilized &amp; Unfertilized NMDS&quot;</span><span class="p">)</span>
<span class="c1"># # plt.tight_layout()</span>
<span class="n">plt</span><span class="o">.</span><span class="n">savefig</span><span class="p">(</span><span class="s2">&quot;figures/AllCombinedNMDS_genes.png&quot;</span><span class="p">,</span><span class="n">bbox_inches</span><span class="o">=</span><span class="s1">&#39;tight&#39;</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">show</span><span class="p">()</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">allCounts</span> <span class="o">=</span> <span class="n">allCounts</span><span class="o">.</span><span class="n">transpose</span><span class="p">()</span>
<span class="n">allCounts</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span><span class="s2">&quot;stats/filteredCountTable.tsv&quot;</span><span class="p">,</span><span class="n">sep</span><span class="o">=</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>        
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="kn">from</span> <span class="nn">matplotlib</span> <span class="k">import</span> <span class="n">cm</span>
<span class="kn">from</span> <span class="nn">matplotlib.colors</span> <span class="k">import</span> <span class="n">ListedColormap</span><span class="p">,</span> <span class="n">LinearSegmentedColormap</span>
<span class="n">viridis</span> <span class="o">=</span> <span class="n">cm</span><span class="o">.</span><span class="n">get_cmap</span><span class="p">(</span><span class="s1">&#39;viridis&#39;</span><span class="p">,</span> <span class="mi">256</span><span class="p">)</span>
<span class="n">newcolors</span> <span class="o">=</span> <span class="n">viridis</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">linspace</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">256</span><span class="p">))</span>
<span class="n">pink</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mi">248</span><span class="o">/</span><span class="mi">256</span><span class="p">,</span> <span class="mi">24</span><span class="o">/</span><span class="mi">256</span><span class="p">,</span> <span class="mi">148</span><span class="o">/</span><span class="mi">256</span><span class="p">,</span> <span class="mi">1</span><span class="p">])</span>
<span class="n">newcolors</span><span class="p">[:</span><span class="mi">25</span><span class="p">,</span> <span class="p">:]</span> <span class="o">=</span> <span class="n">pink</span>
<span class="n">newcmp</span> <span class="o">=</span> <span class="n">ListedColormap</span><span class="p">(</span><span class="n">newcolors</span><span class="p">)</span>
</pre></div>

    </div>
</div>
</div>

  </div>
<div class="cell border-box-sizing text_cell rendered"><div class="inner_cell">
<div class="text_cell_render border-box-sizing rendered_html">
<h1 id="Look-at-annotations">Look at annotations<a class="anchor-link" href="#Look-at-annotations">&#182;</a></h1>
</div>
</div>
</div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">annoMap</span> <span class="o">=</span> <span class="p">{}</span>
<span class="n">revMap</span> <span class="o">=</span> <span class="p">{}</span>
<span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">open</span><span class="p">(</span><span class="s2">&quot;annotations/annotationDescripts.tsv&quot;</span><span class="p">):</span>
    <span class="n">contID</span><span class="p">,</span> <span class="n">function</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">)</span>
<span class="c1">#     if contID in annoMap:</span>
<span class="c1">#         print(contID,function,annoMap[contID])</span>
<span class="c1">#         break</span>
    <span class="n">annoMap</span><span class="p">[</span><span class="n">contID</span><span class="p">]</span><span class="o">=</span> <span class="n">function</span>
    <span class="k">try</span><span class="p">:</span><span class="n">revMap</span><span class="p">[</span><span class="n">function</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">contID</span><span class="p">)</span>
    <span class="k">except</span><span class="p">:</span><span class="n">revMap</span><span class="p">[</span><span class="n">function</span><span class="p">]</span> <span class="o">=</span> <span class="nb">set</span><span class="p">([</span><span class="n">contID</span><span class="p">])</span>
<span class="n">dist</span> <span class="o">=</span> <span class="p">{}</span>
<span class="k">for</span> <span class="n">function</span><span class="p">,</span><span class="n">contigs</span> <span class="ow">in</span> <span class="n">revMap</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
    <span class="n">dist</span><span class="p">[</span><span class="n">function</span><span class="p">]</span><span class="o">=</span><span class="nb">len</span><span class="p">(</span><span class="n">contigs</span><span class="p">)</span>
<span class="n">dist</span> <span class="o">=</span> <span class="n">Series</span><span class="p">(</span><span class="n">dist</span><span class="p">)</span>
<span class="n">dist</span><span class="o">.</span><span class="n">plot</span><span class="o">.</span><span class="n">hist</span><span class="p">();</span>
<span class="n">dump</span><span class="p">(</span><span class="n">revMap</span><span class="p">,</span><span class="nb">open</span><span class="p">(</span><span class="s2">&quot;pickles/functionMap.p&quot;</span><span class="p">,</span><span class="s2">&quot;wb&quot;</span><span class="p">))</span>
<span class="n">dump</span><span class="p">(</span><span class="n">annoMap</span><span class="p">,</span><span class="nb">open</span><span class="p">(</span><span class="s2">&quot;pickles/annoMap.p&quot;</span><span class="p">,</span><span class="s2">&quot;wb&quot;</span><span class="p">))</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">dist</span><span class="p">[</span><span class="n">dist</span><span class="o">&gt;</span><span class="mi">900</span><span class="p">]</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">allCounts</span><span class="o">.</span><span class="n">head</span><span class="p">()</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">revMap</span> <span class="o">=</span> <span class="n">load</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="s2">&quot;pickles/functionMap.p&quot;</span><span class="p">,</span><span class="s2">&quot;rb&quot;</span><span class="p">))</span>
<span class="nb">list</span><span class="p">(</span><span class="n">revMap</span><span class="o">.</span><span class="n">keys</span><span class="p">())[:</span><span class="mi">10</span><span class="p">]</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="kn">from</span> <span class="nn">pickle</span> <span class="k">import</span> <span class="n">load</span><span class="p">,</span><span class="n">dump</span>
<span class="n">allCounts</span> <span class="o">=</span> <span class="n">load</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="s2">&quot;pickles/allCounts_genes.p&quot;</span><span class="p">,</span><span class="s2">&quot;rb&quot;</span><span class="p">))</span>
<span class="n">annoMap</span> <span class="o">=</span> <span class="n">load</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="s2">&quot;pickles/annoMap.p&quot;</span><span class="p">,</span><span class="s2">&quot;rb&quot;</span><span class="p">))</span>
<span class="n">revMap</span> <span class="o">=</span> <span class="n">load</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="s2">&quot;pickles/functionMap.p&quot;</span><span class="p">,</span><span class="s2">&quot;rb&quot;</span><span class="p">))</span>

<span class="n">excCounter</span> <span class="o">=</span> <span class="mi">0</span>
<span class="n">geneCounts</span> <span class="o">=</span> <span class="p">{}</span>
<span class="k">for</span> <span class="n">index</span><span class="p">,</span><span class="n">sample</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">allCounts</span><span class="o">.</span><span class="n">columns</span><span class="p">):</span>
    <span class="n">geneCounts</span><span class="p">[</span><span class="n">sample</span><span class="p">]</span><span class="o">=</span><span class="p">{}</span>
    <span class="n">sampleCounts</span> <span class="o">=</span> <span class="n">allCounts</span><span class="p">[</span><span class="n">sample</span><span class="p">]</span>
    <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;</span><span class="si">%i</span><span class="s2">. </span><span class="si">%s</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">index</span><span class="o">+</span><span class="mi">1</span><span class="p">,</span><span class="n">sample</span><span class="p">))</span>
    <span class="k">for</span> <span class="n">function</span><span class="p">,</span><span class="n">contigs</span> <span class="ow">in</span> <span class="n">revMap</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
        <span class="n">functCounts</span> <span class="o">=</span> <span class="n">sampleCounts</span><span class="p">[</span><span class="n">sampleCounts</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">contigs</span><span class="p">)]</span>
        <span class="n">nReads</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">functCounts</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">axis</span> <span class="o">=</span> <span class="mi">0</span><span class="p">))</span>
        <span class="n">geneCounts</span><span class="p">[</span><span class="n">sample</span><span class="p">][</span><span class="n">function</span><span class="p">]</span> <span class="o">=</span> <span class="n">nReads</span>
<span class="c1">#         try: geneCounts[sample][function] = nReads/len(functCounts)</span>
<span class="c1">#         except:</span>
<span class="c1">#             excCounter +=1</span>
<span class="c1">#             geneCounts[sample][function] = 0.0</span>
<span class="n">dump</span><span class="p">(</span><span class="n">geneCounts</span><span class="p">,</span><span class="nb">open</span><span class="p">(</span><span class="s2">&quot;pickles/pooledGeneCounts.p&quot;</span><span class="p">,</span><span class="s2">&quot;wb&quot;</span><span class="p">))</span>
<span class="nb">print</span><span class="p">(</span><span class="s2">&quot;There were </span><span class="si">%i</span><span class="s2"> genes with no representative contigs&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">excCounter</span><span class="p">))</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">geneCounts</span> <span class="o">=</span> <span class="n">DataFrame</span><span class="p">(</span><span class="n">load</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="s2">&quot;pickles/pooledGeneCounts.p&quot;</span><span class="p">,</span><span class="s2">&quot;rb&quot;</span><span class="p">)))</span>
<span class="nb">print</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">geneCounts</span><span class="p">))</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">geneCounts</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span><span class="s2">&quot;tables/GeneCounts.tsv&quot;</span><span class="p">,</span><span class="n">sep</span><span class="o">=</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">df</span> <span class="o">=</span> <span class="n">DataFrame</span><span class="p">(</span><span class="n">geneCounts</span><span class="p">)</span>
<span class="n">remove</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>

<span class="k">for</span> <span class="n">function</span> <span class="ow">in</span> <span class="n">df</span><span class="o">.</span><span class="n">index</span><span class="p">:</span>
    <span class="n">functionCount</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">df</span><span class="p">[</span><span class="n">df</span><span class="o">.</span><span class="n">index</span> <span class="o">==</span> <span class="n">function</span><span class="p">]</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">))</span> 
    <span class="k">if</span><span class="p">(</span><span class="n">functionCount</span> <span class="o">==</span> <span class="mf">0.0</span><span class="p">):</span> <span class="n">remove</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">function</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">remove</span><span class="p">))</span>
<span class="n">df</span><span class="o">.</span><span class="n">drop</span><span class="p">(</span><span class="n">remove</span><span class="p">,</span><span class="n">inplace</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">df</span><span class="o">.</span><span class="n">head</span><span class="p">()</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">distlist</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">function</span> <span class="ow">in</span> <span class="n">df</span><span class="o">.</span><span class="n">index</span><span class="p">:</span><span class="n">distlist</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">float</span><span class="p">(</span><span class="n">df</span><span class="p">[</span><span class="n">df</span><span class="o">.</span><span class="n">index</span> <span class="o">==</span> <span class="n">function</span><span class="p">]</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">)))</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">dist</span> <span class="o">=</span> <span class="n">Series</span><span class="p">(</span><span class="n">distlist</span><span class="p">)</span>
<span class="n">dist</span> <span class="o">=</span> <span class="n">dist</span><span class="p">[</span><span class="n">dist</span> <span class="o">&lt;</span> <span class="n">dist</span><span class="o">.</span><span class="n">mean</span><span class="p">()</span><span class="o">*.</span><span class="mi">001</span><span class="o">*</span><span class="n">dist</span><span class="o">.</span><span class="n">std</span><span class="p">()]</span>
<span class="n">dist</span><span class="o">.</span><span class="n">plot</span><span class="o">.</span><span class="n">hist</span><span class="p">()</span>
<span class="n">dist</span><span class="o">.</span><span class="n">describe</span><span class="p">()</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">diamondAnnos</span> <span class="o">=</span> <span class="p">{}</span>
<span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">open</span><span class="p">(</span><span class="s2">&quot;KEGG_tools_out/diamondAnnotations_0_KOtable.txt&quot;</span><span class="p">):</span>
    <span class="n">rec</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">)</span>
    <span class="k">try</span><span class="p">:</span> <span class="n">diamondAnnos</span><span class="p">[</span><span class="n">rec</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">rec</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>
    <span class="k">except</span><span class="p">:</span>  <span class="n">diamondAnnos</span><span class="p">[</span><span class="n">rec</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span> <span class="o">=</span> <span class="nb">set</span><span class="p">([</span><span class="n">rec</span><span class="p">[</span><span class="mi">2</span><span class="p">]])</span>
<span class="nb">print</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">diamondAnnos</span><span class="p">))</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">dist</span><span class="p">,</span><span class="n">conts</span> <span class="o">=</span> <span class="p">[],[]</span>
<span class="k">for</span> <span class="n">contID</span><span class="p">,</span> <span class="n">KOList</span> <span class="ow">in</span> <span class="n">diamondAnnos</span><span class="o">.</span><span class="n">items</span><span class="p">():</span> <span class="n">conts</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">contID</span><span class="p">);</span> <span class="n">dist</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">KOList</span><span class="p">))</span>
<span class="n">dist</span> <span class="o">=</span> <span class="n">Series</span><span class="p">(</span><span class="n">dist</span><span class="p">,</span><span class="n">index</span><span class="o">=</span><span class="n">conts</span><span class="p">)</span>
<span class="n">dist</span><span class="o">.</span><span class="n">plot</span><span class="o">.</span><span class="n">hist</span><span class="p">()</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="nb">len</span><span class="p">(</span><span class="n">dist</span><span class="p">[</span><span class="n">dist</span><span class="o">&gt;=</span><span class="mi">2</span><span class="p">])</span><span class="o">/</span><span class="nb">float</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">dist</span><span class="p">))</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">allCounts</span> <span class="o">=</span> <span class="n">load</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="s2">&quot;pickles/allCounts_genes.p&quot;</span><span class="p">,</span><span class="s2">&quot;rb&quot;</span><span class="p">))</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">medianReplicateGeneCounts</span> <span class="o">=</span> <span class="p">{}</span>
<span class="k">for</span> <span class="n">crop</span> <span class="ow">in</span> <span class="nb">set</span><span class="p">(</span><span class="n">metadata</span><span class="o">.</span><span class="n">type</span><span class="p">):</span>
    <span class="k">for</span> <span class="n">date</span> <span class="ow">in</span> <span class="nb">set</span><span class="p">(</span><span class="n">metadata</span><span class="o">.</span><span class="n">sampling_date</span><span class="p">):</span>
        <span class="k">for</span> <span class="n">treatment</span> <span class="ow">in</span> <span class="nb">set</span><span class="p">(</span><span class="n">metadata</span><span class="o">.</span><span class="n">treatment</span><span class="p">):</span>
            <span class="n">replicateSamples</span> <span class="o">=</span> <span class="n">metadata</span><span class="o">.</span><span class="n">loc</span><span class="p">[(</span><span class="n">metadata</span><span class="o">.</span><span class="n">sampling_date</span><span class="o">==</span><span class="n">date</span><span class="p">)</span> <span class="o">&amp;</span> <span class="p">(</span><span class="n">metadata</span><span class="o">.</span><span class="n">treatment</span><span class="o">==</span><span class="n">treatment</span><span class="p">)</span> <span class="o">&amp;</span> <span class="p">(</span><span class="n">metadata</span><span class="o">.</span><span class="n">type</span> <span class="o">==</span> <span class="n">crop</span><span class="p">)]</span>
            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">replicateSamples</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span> <span class="k">continue</span>
<span class="c1">#             print(crop,date,treatment)</span>
            <span class="n">replicateCounts</span> <span class="o">=</span> <span class="n">geneCounts</span><span class="p">[</span><span class="nb">list</span><span class="p">(</span><span class="n">replicateSamples</span><span class="o">.</span><span class="n">nucleic_acid_name</span><span class="p">)]</span>
            <span class="n">groupID</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">replicateSamples</span><span class="o">.</span><span class="n">nucleic_acid_name</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;R1&quot;</span><span class="p">,</span><span class="s2">&quot;&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;R2&quot;</span><span class="p">,</span><span class="s2">&quot;&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;R3&quot;</span><span class="p">,</span><span class="s2">&quot;&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;R4&quot;</span><span class="p">,</span><span class="s2">&quot;&quot;</span><span class="p">)</span>
            <span class="n">medianReplicateGeneCounts</span><span class="p">[</span><span class="n">groupID</span><span class="p">]</span> <span class="o">=</span> <span class="n">replicateCounts</span><span class="o">.</span><span class="n">median</span><span class="p">(</span><span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
            <span class="c1">#             </span>
<span class="c1">#             sampleGroup[groupID] = {}</span>
<span class="c1">#             for function, contigList in revMap.items():</span>
<span class="c1">#                 functionCounts = sampleCounts[sampleCounts.index.isin(contigList)]</span>
<span class="c1">#                 sampleGroup[groupID][function] = functionCounts.sum().median()</span>
<span class="n">medianReplicateGeneCounts</span> <span class="o">=</span> <span class="n">DataFrame</span><span class="p">(</span><span class="n">medianReplicateGeneCounts</span><span class="p">)</span>
<span class="n">medianReplicateGeneCounts</span><span class="o">.</span><span class="n">head</span><span class="p">()</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">remove</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
<span class="k">for</span> <span class="n">function</span> <span class="ow">in</span> <span class="n">medianReplicateGeneCounts</span><span class="o">.</span><span class="n">index</span><span class="p">:</span>
    <span class="k">if</span> <span class="n">medianReplicateGeneCounts</span><span class="p">[</span><span class="n">medianReplicateGeneCounts</span><span class="o">.</span><span class="n">index</span> <span class="o">==</span> <span class="n">function</span><span class="p">]</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span><span class="o">.</span><span class="n">sum</span><span class="p">()</span><span class="o">==</span> <span class="mi">0</span><span class="p">:</span><span class="n">remove</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">function</span><span class="p">)</span>
<span class="nb">len</span><span class="p">(</span><span class="n">remove</span><span class="p">)</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="nb">print</span><span class="p">(</span><span class="n">medianReplicateGeneCounts</span><span class="o">.</span><span class="n">shape</span><span class="p">)</span>
<span class="n">medianReplicateGeneCounts</span><span class="o">.</span><span class="n">drop</span><span class="p">(</span><span class="n">remove</span><span class="p">,</span><span class="n">inplace</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="n">medianReplicateGeneCounts</span><span class="o">.</span><span class="n">shape</span><span class="p">)</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">dump</span><span class="p">(</span><span class="n">sampleGroup</span><span class="p">,</span><span class="nb">open</span><span class="p">(</span><span class="s2">&quot;pickles/deepFunctionReplicateCounts.p&quot;</span><span class="p">,</span><span class="s2">&quot;wb&quot;</span><span class="p">))</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">medianReplicateGeneCounts</span><span class="o">.</span><span class="n">shape</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">dates</span><span class="o">=</span><span class="n">metadata</span><span class="p">[[</span><span class="s2">&quot;sampling_date&quot;</span><span class="p">,</span><span class="s2">&quot;Date&quot;</span><span class="p">,</span><span class="s2">&quot;nucleic_acid_name&quot;</span><span class="p">]]</span>
<span class="n">dates</span><span class="o">=</span><span class="n">dates</span><span class="o">.</span><span class="n">sort_values</span><span class="p">(</span><span class="n">by</span><span class="o">=</span><span class="s2">&quot;Date&quot;</span><span class="p">)</span>
<span class="n">dates</span><span class="o">=</span><span class="n">dates</span><span class="p">[[</span><span class="s2">&quot;sampling_date&quot;</span><span class="p">,</span><span class="s2">&quot;nucleic_acid_name&quot;</span><span class="p">]]</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">metadata</span> <span class="o">=</span> <span class="n">metadata</span><span class="o">.</span><span class="n">sort_values</span><span class="p">(</span><span class="n">by</span><span class="o">=</span><span class="s2">&quot;Date&quot;</span><span class="p">)</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">metadata</span><span class="o">.</span><span class="n">treatment</span><span class="o">.</span><span class="n">unique</span><span class="p">()</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">persistent</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
<span class="n">crop</span> <span class="o">=</span><span class="s2">&quot;G5&quot;</span>
<span class="n">treatment</span> <span class="o">=</span> <span class="s1">&#39;standard fertilization&#39;</span>
<span class="n">prevTimePoint</span> <span class="o">=</span> <span class="p">[]</span>
<span class="n">seenGenes</span> <span class="o">=</span><span class="nb">set</span><span class="p">()</span>
<span class="k">for</span> <span class="n">crop</span> <span class="ow">in</span> <span class="n">metadata</span><span class="o">.</span><span class="n">type</span><span class="o">.</span><span class="n">unique</span><span class="p">():</span>
    <span class="k">for</span> <span class="n">treatment</span> <span class="ow">in</span> <span class="n">metadata</span><span class="o">.</span><span class="n">treatment</span><span class="o">.</span><span class="n">unique</span><span class="p">():</span>
        <span class="k">for</span> <span class="n">date</span> <span class="ow">in</span> <span class="n">dates</span><span class="o">.</span><span class="n">sampling_date</span><span class="o">.</span><span class="n">unique</span><span class="p">():</span>
            <span class="n">replicateSamples</span> <span class="o">=</span> <span class="n">metadata</span><span class="o">.</span><span class="n">loc</span><span class="p">[(</span><span class="n">metadata</span><span class="o">.</span><span class="n">sampling_date</span><span class="o">==</span><span class="n">date</span><span class="p">)</span> <span class="o">&amp;</span> <span class="p">(</span><span class="n">metadata</span><span class="o">.</span><span class="n">treatment</span><span class="o">==</span><span class="n">treatment</span><span class="p">)</span> <span class="o">&amp;</span> <span class="p">(</span><span class="n">metadata</span><span class="o">.</span><span class="n">type</span> <span class="o">==</span> <span class="n">crop</span><span class="p">)]</span>
            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">replicateSamples</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span> <span class="k">continue</span>
            <span class="n">groupID</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">replicateSamples</span><span class="o">.</span><span class="n">nucleic_acid_name</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;R1&quot;</span><span class="p">,</span><span class="s2">&quot;&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;R2&quot;</span><span class="p">,</span><span class="s2">&quot;&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;R3&quot;</span><span class="p">,</span><span class="s2">&quot;&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;R4&quot;</span><span class="p">,</span><span class="s2">&quot;&quot;</span><span class="p">)</span>
            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">prevTimePoint</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
                <span class="n">prevTimePoint</span> <span class="o">=</span> <span class="n">medianReplicateGeneCounts</span><span class="p">[</span><span class="n">groupID</span><span class="p">]</span>
                <span class="n">prevTimePoint</span> <span class="o">=</span> <span class="n">prevTimePoint</span><span class="p">[</span><span class="n">prevTimePoint</span><span class="o">&gt;</span><span class="mi">0</span><span class="p">]</span>
                <span class="n">persistent</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="n">prevTimePoint</span><span class="o">.</span><span class="n">index</span><span class="p">)</span>
        <span class="c1">#         print(&quot;There are %i genes present at start %s&quot; % (len(prevTimePoint),str(date)))</span>
                <span class="k">continue</span>
            <span class="n">curTimePoint</span> <span class="o">=</span> <span class="n">medianReplicateGeneCounts</span><span class="p">[</span><span class="n">groupID</span><span class="p">]</span>
            <span class="n">curTimePoint</span> <span class="o">=</span> <span class="n">curTimePoint</span><span class="p">[</span><span class="n">curTimePoint</span><span class="o">&gt;</span><span class="mi">0</span><span class="p">]</span>
        <span class="c1">#     print(&quot;At the next time point %s there are %i genes&quot;%(str(date),len(curTimePoint)))</span>
        <span class="c1">#     print(&quot;\t%i genes existed in the last timepoint&quot; % (len(set(curTimePoint.index).intersection(prevTimePoint.index))))</span>
        <span class="c1">#     print(&quot;\t%i genes are new&quot; % (len(set(curTimePoint.index).difference(prevTimePoint.index))))</span>
            <span class="n">seenGenes</span> <span class="o">=</span> <span class="n">seenGenes</span><span class="o">.</span><span class="n">union</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">curTimePoint</span><span class="o">.</span><span class="n">index</span><span class="p">)</span><span class="o">.</span><span class="n">union</span><span class="p">(</span><span class="n">prevTimePoint</span><span class="o">.</span><span class="n">index</span><span class="p">))</span>
        <span class="c1">#     print(&quot;\t%i genes so far\n&quot; % (len(seenGenes)))</span>
            <span class="n">persistent</span> <span class="o">=</span> <span class="n">persistent</span><span class="o">.</span><span class="n">intersection</span><span class="p">(</span><span class="n">curTimePoint</span><span class="o">.</span><span class="n">index</span><span class="p">)</span>
            <span class="n">prevTimePoint</span> <span class="o">=</span> <span class="n">curTimePoint</span>
        <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;There are </span><span class="si">%i</span><span class="s2"> genes that persist over time for </span><span class="si">%s</span><span class="s2"> with </span><span class="si">%s</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">persistent</span><span class="p">),</span><span class="n">crop</span><span class="p">,</span><span class="n">treatment</span><span class="p">))</span>
        <span class="n">persIncreasing</span> <span class="o">=</span> <span class="n">persistent</span>
        <span class="n">persDecreasing</span> <span class="o">=</span> <span class="n">persistent</span>
        <span class="n">prevTimePoint</span> <span class="o">=</span> <span class="p">[]</span>
        <span class="n">seenGenes</span> <span class="o">=</span><span class="nb">set</span><span class="p">()</span>
        <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">date</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">dates</span><span class="o">.</span><span class="n">sampling_date</span><span class="o">.</span><span class="n">unique</span><span class="p">()):</span>
            <span class="n">replicateSamples</span> <span class="o">=</span> <span class="n">metadata</span><span class="o">.</span><span class="n">loc</span><span class="p">[(</span><span class="n">metadata</span><span class="o">.</span><span class="n">sampling_date</span><span class="o">==</span><span class="n">date</span><span class="p">)</span> <span class="o">&amp;</span> <span class="p">(</span><span class="n">metadata</span><span class="o">.</span><span class="n">treatment</span><span class="o">==</span><span class="n">treatment</span><span class="p">)</span> <span class="o">&amp;</span> <span class="p">(</span><span class="n">metadata</span><span class="o">.</span><span class="n">type</span> <span class="o">==</span> <span class="n">crop</span><span class="p">)]</span>
            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">replicateSamples</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span> <span class="k">continue</span>
            <span class="n">groupID</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">replicateSamples</span><span class="o">.</span><span class="n">nucleic_acid_name</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;R1&quot;</span><span class="p">,</span><span class="s2">&quot;&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;R2&quot;</span><span class="p">,</span><span class="s2">&quot;&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;R3&quot;</span><span class="p">,</span><span class="s2">&quot;&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;R4&quot;</span><span class="p">,</span><span class="s2">&quot;&quot;</span><span class="p">)</span>
            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">prevTimePoint</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
                <span class="n">prevTimePoint</span> <span class="o">=</span> <span class="n">medianReplicateGeneCounts</span><span class="p">[</span><span class="n">groupID</span><span class="p">]</span>
                <span class="n">prevTimePointDec</span> <span class="o">=</span> <span class="n">prevTimePoint</span><span class="p">[</span><span class="n">prevTimePoint</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">persistent</span><span class="p">)]</span>
                <span class="n">prevTimePointInc</span> <span class="o">=</span> <span class="n">prevTimePoint</span><span class="p">[</span><span class="n">prevTimePoint</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">persistent</span><span class="p">)]</span>
                <span class="k">continue</span>
            <span class="n">prevTimePointInc</span> <span class="o">=</span> <span class="n">prevTimePointInc</span><span class="p">[</span><span class="n">prevTimePointInc</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">persIncreasing</span><span class="p">)]</span>
            <span class="n">prevTimePointDec</span> <span class="o">=</span> <span class="n">prevTimePointDec</span><span class="p">[</span><span class="n">prevTimePointDec</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">persDecreasing</span><span class="p">)]</span>
            <span class="n">curTimePoint</span> <span class="o">=</span> <span class="n">medianReplicateGeneCounts</span><span class="p">[</span><span class="n">groupID</span><span class="p">]</span>
            <span class="n">curIncreasing</span> <span class="o">=</span> <span class="n">curTimePoint</span><span class="p">[</span><span class="n">curTimePoint</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">persIncreasing</span><span class="p">)]</span>
            <span class="n">curDecreasing</span> <span class="o">=</span> <span class="n">curTimePoint</span><span class="p">[</span><span class="n">curTimePoint</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">persDecreasing</span><span class="p">)]</span>
            <span class="n">increasing</span> <span class="o">=</span> <span class="n">curIncreasing</span><span class="p">[</span><span class="n">curIncreasing</span> <span class="o">&gt;=</span> <span class="n">prevTimePointInc</span><span class="p">]</span>
            <span class="n">decreasing</span> <span class="o">=</span> <span class="n">curDecreasing</span><span class="p">[</span><span class="n">curDecreasing</span> <span class="o">&lt;=</span> <span class="n">prevTimePointDec</span><span class="p">]</span>
            <span class="n">persIncreasing</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="n">increasing</span><span class="o">.</span><span class="n">index</span><span class="p">)</span>
            <span class="n">persDecreasing</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="n">decreasing</span><span class="o">.</span><span class="n">index</span><span class="p">)</span>
            <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;</span><span class="se">\t</span><span class="s2">At time </span><span class="si">%s</span><span class="s2"> </span><span class="se">\t</span><span class="s2"> </span><span class="si">%i</span><span class="s2"> genes are still increasing</span><span class="se">\t</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">date</span><span class="p">),</span> <span class="nb">len</span><span class="p">(</span><span class="n">persIncreasing</span><span class="p">)),</span><span class="n">end</span><span class="o">=</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
            <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;</span><span class="si">%i</span><span class="s2"> genes are still decreasing&quot;</span> <span class="o">%</span> <span class="p">(</span> <span class="nb">len</span><span class="p">(</span><span class="n">persDecreasing</span><span class="p">)))</span>
            
            <span class="c1">#Add normalization by number of reads</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">date</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">dates</span><span class="o">.</span><span class="n">sampling_date</span><span class="o">.</span><span class="n">unique</span><span class="p">()):</span><span class="nb">print</span><span class="p">(</span><span class="n">date</span><span class="p">)</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">persistent</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
<span class="n">crop</span> <span class="o">=</span><span class="s2">&quot;G6&quot;</span>
<span class="n">prevTimePoint</span> <span class="o">=</span> <span class="p">[]</span>
<span class="n">seenGenes</span> <span class="o">=</span><span class="nb">set</span><span class="p">()</span>
<span class="k">for</span> <span class="n">date</span> <span class="ow">in</span> <span class="n">dates</span><span class="o">.</span><span class="n">sampling_date</span><span class="o">.</span><span class="n">unique</span><span class="p">():</span>
    <span class="n">replicateSamples</span> <span class="o">=</span> <span class="n">metadata</span><span class="o">.</span><span class="n">loc</span><span class="p">[(</span><span class="n">metadata</span><span class="o">.</span><span class="n">sampling_date</span><span class="o">==</span><span class="n">date</span><span class="p">)</span> <span class="o">&amp;</span> <span class="p">(</span><span class="n">metadata</span><span class="o">.</span><span class="n">treatment</span><span class="o">==</span><span class="n">treatment</span><span class="p">)</span> <span class="o">&amp;</span> <span class="p">(</span><span class="n">metadata</span><span class="o">.</span><span class="n">type</span> <span class="o">==</span> <span class="n">crop</span><span class="p">)]</span>
    <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">replicateSamples</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span> <span class="k">continue</span>
    <span class="n">groupID</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">replicateSamples</span><span class="o">.</span><span class="n">nucleic_acid_name</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;R1&quot;</span><span class="p">,</span><span class="s2">&quot;&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;R2&quot;</span><span class="p">,</span><span class="s2">&quot;&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;R3&quot;</span><span class="p">,</span><span class="s2">&quot;&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;R4&quot;</span><span class="p">,</span><span class="s2">&quot;&quot;</span><span class="p">)</span>
    <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">prevTimePoint</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
        <span class="n">prevTimePoint</span> <span class="o">=</span> <span class="n">medianReplicateGeneCounts</span><span class="p">[</span><span class="n">groupID</span><span class="p">]</span>
        <span class="n">prevTimePoint</span> <span class="o">=</span> <span class="n">prevTimePoint</span><span class="p">[</span><span class="n">prevTimePoint</span><span class="o">&gt;</span><span class="mi">0</span><span class="p">]</span>
        <span class="n">persistent</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="n">prevTimePoint</span><span class="o">.</span><span class="n">index</span><span class="p">)</span>
        <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;There are </span><span class="si">%i</span><span class="s2"> genes present at start </span><span class="si">%s</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">prevTimePoint</span><span class="p">),</span><span class="nb">str</span><span class="p">(</span><span class="n">date</span><span class="p">)))</span>
        <span class="k">continue</span>
    <span class="n">curTimePoint</span> <span class="o">=</span> <span class="n">medianReplicateGeneCounts</span><span class="p">[</span><span class="n">groupID</span><span class="p">]</span>
    <span class="n">curTimePoint</span> <span class="o">=</span> <span class="n">curTimePoint</span><span class="p">[</span><span class="n">curTimePoint</span><span class="o">&gt;</span><span class="mi">0</span><span class="p">]</span>
    <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;At the next time point </span><span class="si">%s</span><span class="s2"> there are </span><span class="si">%i</span><span class="s2"> genes&quot;</span><span class="o">%</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">date</span><span class="p">),</span><span class="nb">len</span><span class="p">(</span><span class="n">curTimePoint</span><span class="p">)))</span>
    <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;</span><span class="se">\t</span><span class="si">%i</span><span class="s2"> genes existed in the last timepoint&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">curTimePoint</span><span class="o">.</span><span class="n">index</span><span class="p">)</span><span class="o">.</span><span class="n">intersection</span><span class="p">(</span><span class="n">prevTimePoint</span><span class="o">.</span><span class="n">index</span><span class="p">))))</span>
    <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;</span><span class="se">\t</span><span class="si">%i</span><span class="s2"> genes are new&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">curTimePoint</span><span class="o">.</span><span class="n">index</span><span class="p">)</span><span class="o">.</span><span class="n">difference</span><span class="p">(</span><span class="n">prevTimePoint</span><span class="o">.</span><span class="n">index</span><span class="p">))))</span>
    <span class="n">seenGenes</span> <span class="o">=</span> <span class="n">seenGenes</span><span class="o">.</span><span class="n">union</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">curTimePoint</span><span class="o">.</span><span class="n">index</span><span class="p">)</span><span class="o">.</span><span class="n">union</span><span class="p">(</span><span class="n">prevTimePoint</span><span class="o">.</span><span class="n">index</span><span class="p">))</span>
    <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;</span><span class="se">\t</span><span class="si">%i</span><span class="s2"> genes so far</span><span class="se">\n</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">seenGenes</span><span class="p">)))</span>
    <span class="n">persistent</span> <span class="o">=</span> <span class="n">persistent</span><span class="o">.</span><span class="n">intersection</span><span class="p">(</span><span class="n">curTimePoint</span><span class="o">.</span><span class="n">index</span><span class="p">)</span>
    <span class="n">prevTimePoint</span> <span class="o">=</span> <span class="n">curTimePoint</span>
<span class="nb">print</span><span class="p">(</span><span class="s2">&quot;There are </span><span class="si">%i</span><span class="s2"> genes that persist over time&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">persistent</span><span class="p">)))</span>
</pre></div>

    </div>
</div>
</div>

  </div>
<div class="cell border-box-sizing text_cell rendered"><div class="inner_cell">
<div class="text_cell_render border-box-sizing rendered_html">
<h3 id="What-genes-consistently-go-up-over-time?">What genes consistently go up over time?<a class="anchor-link" href="#What-genes-consistently-go-up-over-time?">&#182;</a></h3>
</div>
</div>
</div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">persIncreasing</span> <span class="o">=</span> <span class="n">persistent</span>
<span class="n">persDecreasing</span> <span class="o">=</span> <span class="n">persistent</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="c1"># persistent</span>
<span class="n">persIncreasing</span> <span class="o">=</span> <span class="n">persistent</span>
<span class="n">persDecreasing</span> <span class="o">=</span> <span class="n">persistent</span>
<span class="n">prevTimePoint</span> <span class="o">=</span> <span class="p">[]</span>
<span class="n">seenGenes</span> <span class="o">=</span><span class="nb">set</span><span class="p">()</span>
<span class="nb">print</span><span class="p">(</span><span class="n">crop</span><span class="p">,</span><span class="n">treatment</span><span class="p">)</span>
<span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">date</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">dates</span><span class="o">.</span><span class="n">sampling_date</span><span class="o">.</span><span class="n">unique</span><span class="p">()):</span>
    <span class="n">replicateSamples</span> <span class="o">=</span> <span class="n">metadata</span><span class="o">.</span><span class="n">loc</span><span class="p">[(</span><span class="n">metadata</span><span class="o">.</span><span class="n">sampling_date</span><span class="o">==</span><span class="n">date</span><span class="p">)</span> <span class="o">&amp;</span> <span class="p">(</span><span class="n">metadata</span><span class="o">.</span><span class="n">treatment</span><span class="o">==</span><span class="n">treatment</span><span class="p">)</span> <span class="o">&amp;</span> <span class="p">(</span><span class="n">metadata</span><span class="o">.</span><span class="n">type</span> <span class="o">==</span> <span class="n">crop</span><span class="p">)]</span>
    <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">replicateSamples</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span> <span class="k">continue</span>
    <span class="n">groupID</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">replicateSamples</span><span class="o">.</span><span class="n">nucleic_acid_name</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;R1&quot;</span><span class="p">,</span><span class="s2">&quot;&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;R2&quot;</span><span class="p">,</span><span class="s2">&quot;&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;R3&quot;</span><span class="p">,</span><span class="s2">&quot;&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;R4&quot;</span><span class="p">,</span><span class="s2">&quot;&quot;</span><span class="p">)</span>
<span class="c1">#     print(groupID)</span>
    <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">prevTimePoint</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
        <span class="n">prevTimePoint</span> <span class="o">=</span> <span class="n">medianReplicateGeneCounts</span><span class="p">[</span><span class="n">groupID</span><span class="p">]</span>
        <span class="n">prevTimePointDec</span> <span class="o">=</span> <span class="n">prevTimePoint</span><span class="p">[</span><span class="n">prevTimePoint</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">persistent</span><span class="p">)]</span>
        <span class="n">prevTimePointInc</span> <span class="o">=</span> <span class="n">prevTimePoint</span><span class="p">[</span><span class="n">prevTimePoint</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">persistent</span><span class="p">)]</span>
        <span class="k">continue</span>
    
    <span class="n">prevTimePointInc</span> <span class="o">=</span> <span class="n">prevTimePointInc</span><span class="p">[</span><span class="n">prevTimePointInc</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">persIncreasing</span><span class="p">)]</span>
    <span class="n">prevTimePointDec</span> <span class="o">=</span> <span class="n">prevTimePointDec</span><span class="p">[</span><span class="n">prevTimePointDec</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">persDecreasing</span><span class="p">)]</span>
    <span class="n">curTimePoint</span> <span class="o">=</span> <span class="n">medianReplicateGeneCounts</span><span class="p">[</span><span class="n">groupID</span><span class="p">]</span>
    <span class="n">curIncreasing</span> <span class="o">=</span> <span class="n">curTimePoint</span><span class="p">[</span><span class="n">curTimePoint</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">persIncreasing</span><span class="p">)]</span>
    <span class="n">curDecreasing</span> <span class="o">=</span> <span class="n">curTimePoint</span><span class="p">[</span><span class="n">curTimePoint</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">persDecreasing</span><span class="p">)]</span>
    <span class="n">increasing</span> <span class="o">=</span> <span class="n">curIncreasing</span><span class="p">[</span><span class="n">curIncreasing</span> <span class="o">&gt;=</span> <span class="n">prevTimePointInc</span><span class="p">]</span>
    <span class="n">decreasing</span> <span class="o">=</span> <span class="n">curDecreasing</span><span class="p">[</span><span class="n">curDecreasing</span> <span class="o">&lt;=</span> <span class="n">prevTimePointDec</span><span class="p">]</span>
    <span class="n">persIncreasing</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="n">increasing</span><span class="o">.</span><span class="n">index</span><span class="p">)</span>
    <span class="n">persDecreasing</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="n">decreasing</span><span class="o">.</span><span class="n">index</span><span class="p">)</span>
    <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;At time </span><span class="si">%i</span><span class="s2"> - </span><span class="si">%i</span><span class="s2"> genes are still increasing&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">persIncreasing</span><span class="p">)),</span><span class="n">end</span><span class="o">=</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
    <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;At time </span><span class="si">%i</span><span class="s2"> - </span><span class="si">%i</span><span class="s2"> genes are still decreasing&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">persDecreasing</span><span class="p">)))</span>
        
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">persIncreasing</span> <span class="o">=</span> <span class="n">persistent</span>
<span class="n">persDecreasing</span> <span class="o">=</span> <span class="n">persistent</span>
<span class="n">prevTimePoint</span> <span class="o">=</span> <span class="p">[]</span>
<span class="n">seenGenes</span> <span class="o">=</span><span class="nb">set</span><span class="p">()</span>
<span class="nb">print</span><span class="p">(</span><span class="n">crop</span><span class="p">,</span><span class="n">treatment</span><span class="p">)</span>
<span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">date</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">dates</span><span class="o">.</span><span class="n">sampling_date</span><span class="o">.</span><span class="n">unique</span><span class="p">()):</span>
    <span class="n">replicateSamples</span> <span class="o">=</span> <span class="n">metadata</span><span class="o">.</span><span class="n">loc</span><span class="p">[(</span><span class="n">metadata</span><span class="o">.</span><span class="n">sampling_date</span><span class="o">==</span><span class="n">date</span><span class="p">)</span> <span class="o">&amp;</span> <span class="p">(</span><span class="n">metadata</span><span class="o">.</span><span class="n">treatment</span><span class="o">==</span><span class="n">treatment</span><span class="p">)</span> <span class="o">&amp;</span> <span class="p">(</span><span class="n">metadata</span><span class="o">.</span><span class="n">type</span> <span class="o">==</span> <span class="n">crop</span><span class="p">)]</span>
    <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">replicateSamples</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span> <span class="k">continue</span>
    <span class="n">groupID</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">replicateSamples</span><span class="o">.</span><span class="n">nucleic_acid_name</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;R1&quot;</span><span class="p">,</span><span class="s2">&quot;&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;R2&quot;</span><span class="p">,</span><span class="s2">&quot;&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;R3&quot;</span><span class="p">,</span><span class="s2">&quot;&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;R4&quot;</span><span class="p">,</span><span class="s2">&quot;&quot;</span><span class="p">)</span>
<span class="c1">#     print(groupID)</span>
    <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">prevTimePoint</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
        <span class="n">prevTimePoint</span> <span class="o">=</span> <span class="n">medianReplicateGeneCounts</span><span class="p">[</span><span class="n">groupID</span><span class="p">]</span>
        <span class="n">prevTimePointDec</span> <span class="o">=</span> <span class="n">prevTimePoint</span><span class="p">[</span><span class="n">prevTimePoint</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">persistent</span><span class="p">)]</span>
        <span class="n">prevTimePointInc</span> <span class="o">=</span> <span class="n">prevTimePoint</span><span class="p">[</span><span class="n">prevTimePoint</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">persistent</span><span class="p">)]</span>
        <span class="k">continue</span>
    
    <span class="n">prevTimePointInc</span> <span class="o">=</span> <span class="n">prevTimePointInc</span><span class="p">[</span><span class="n">prevTimePointInc</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">persIncreasing</span><span class="p">)]</span>
    <span class="n">prevTimePointDec</span> <span class="o">=</span> <span class="n">prevTimePointDec</span><span class="p">[</span><span class="n">prevTimePointDec</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">persDecreasing</span><span class="p">)]</span>
    <span class="n">curTimePoint</span> <span class="o">=</span> <span class="n">medianReplicateGeneCounts</span><span class="p">[</span><span class="n">groupID</span><span class="p">]</span>
    <span class="n">curIncreasing</span> <span class="o">=</span> <span class="n">curTimePoint</span><span class="p">[</span><span class="n">curTimePoint</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">persIncreasing</span><span class="p">)]</span>
    <span class="n">curDecreasing</span> <span class="o">=</span> <span class="n">curTimePoint</span><span class="p">[</span><span class="n">curTimePoint</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">persDecreasing</span><span class="p">)]</span>
    <span class="n">increasing</span> <span class="o">=</span> <span class="n">curIncreasing</span><span class="p">[</span><span class="n">curIncreasing</span> <span class="o">&gt;=</span> <span class="n">prevTimePointInc</span><span class="p">]</span>
    <span class="n">decreasing</span> <span class="o">=</span> <span class="n">curDecreasing</span><span class="p">[</span><span class="n">curDecreasing</span> <span class="o">&lt;=</span> <span class="n">prevTimePointDec</span><span class="p">]</span>
    <span class="n">persIncreasing</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="n">increasing</span><span class="o">.</span><span class="n">index</span><span class="p">)</span>
    <span class="n">persDecreasing</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="n">decreasing</span><span class="o">.</span><span class="n">index</span><span class="p">)</span>
    <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;At time </span><span class="si">%i</span><span class="s2"> - </span><span class="si">%i</span><span class="s2"> genes are still increasing&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">persIncreasing</span><span class="p">)),</span><span class="n">end</span><span class="o">=</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
    <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;At time </span><span class="si">%i</span><span class="s2"> - </span><span class="si">%i</span><span class="s2"> genes are still decreasing&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">persDecreasing</span><span class="p">)))</span>
        
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">startTime</span> <span class="o">=</span> <span class="n">medianReplicateGeneCounts</span><span class="p">[</span><span class="s1">&#39;G5_NF_09MAY2016_LD1&#39;</span><span class="p">]</span>
<span class="n">startTime</span> <span class="o">=</span> <span class="n">startTime</span><span class="p">[</span><span class="n">startTime</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">]</span>
<span class="nb">print</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">startTime</span><span class="p">))</span>
<span class="n">startTime</span><span class="o">.</span><span class="n">index</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">curTimePoint</span><span class="p">[</span><span class="n">curTimePoint</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">persDecreasing</span><span class="p">)]</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">seqMappedDist</span> <span class="o">=</span> <span class="n">Series</span><span class="p">(</span><span class="n">load</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="s2">&quot;pickles/seqMappedCounter.p&quot;</span><span class="p">,</span><span class="s2">&quot;rb&quot;</span><span class="p">)))</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">presenceDist</span><span class="o">=</span><span class="n">presenceDist</span><span class="o">/</span><span class="nb">float</span><span class="p">(</span><span class="n">numSamples</span><span class="p">)</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="c1">#fh = open(&quot;assemblies/parts/final.contigs.%i.fa&quot; % (index),&quot;w&quot;)</span>
<span class="kn">from</span> <span class="nn">Bio.SeqIO</span> <span class="k">import</span> <span class="n">parse</span><span class="p">,</span> <span class="n">write</span>
<span class="n">counter</span><span class="p">,</span><span class="n">index</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span>
<span class="k">for</span> <span class="n">rec</span> <span class="ow">in</span> <span class="n">parse</span><span class="p">(</span><span class="s2">&quot;assemblies/final.contigs.fa&quot;</span><span class="p">,</span><span class="s2">&quot;fasta&quot;</span><span class="p">):</span> 
    <span class="k">if</span> <span class="n">counter</span> <span class="o">%</span> <span class="mi">500000</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
        <span class="c1">#fh.close()</span>
        <span class="n">index</span> <span class="o">+=</span> <span class="mi">1</span>
        <span class="nb">print</span><span class="p">(</span><span class="n">index</span><span class="p">,</span><span class="n">end</span><span class="o">=</span><span class="s2">&quot; &quot;</span><span class="p">)</span>
        <span class="c1">#fh = open(&quot;assemblies/parts/final.contigs.%i.fa&quot; % (index),&quot;w&quot;)</span>
    <span class="c1">#write(rec,fh,&quot;fasta&quot;)</span>
    <span class="n">counter</span><span class="o">+=</span><span class="mi">1</span>
<span class="c1">#fh.close()     </span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span> 
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span>%%bash
<span class="c1">#ls -laht pickles</span>
<span class="c1">#head stats/11425.5.206700.GCCTTGT-AACAAGG.fastq.gz.tsv</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="c1">#Initialize the dictionary for the counts</span>
<span class="n">seqCounter</span> <span class="o">=</span> <span class="p">{}</span> <span class="c1">#load(open(&quot;pickles/seqCounter.p&quot;,&quot;rb&quot;))</span>
<span class="n">combined_abundance</span> <span class="o">=</span> <span class="n">seqCounter</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
<span class="k">for</span> <span class="n">crop</span> <span class="ow">in</span> <span class="nb">set</span><span class="p">(</span><span class="n">metadata</span><span class="o">.</span><span class="n">type</span><span class="p">):</span>
    <span class="k">for</span> <span class="n">date</span> <span class="ow">in</span> <span class="nb">set</span><span class="p">(</span><span class="n">metadata</span><span class="o">.</span><span class="n">sampling_date</span><span class="p">):</span>
        <span class="k">for</span> <span class="n">treatment</span> <span class="ow">in</span> <span class="nb">set</span><span class="p">(</span><span class="n">metadata</span><span class="o">.</span><span class="n">treatment</span><span class="p">):</span>
            <span class="n">sampleGroupMeta</span> <span class="o">=</span> <span class="n">metadata</span><span class="o">.</span><span class="n">loc</span><span class="p">[(</span><span class="n">metadata</span><span class="o">.</span><span class="n">sampling_date</span><span class="o">==</span><span class="n">date</span><span class="p">)</span> <span class="o">&amp;</span> <span class="p">(</span><span class="n">metadata</span><span class="o">.</span><span class="n">treatment</span><span class="o">==</span><span class="n">treatment</span><span class="p">)</span> <span class="o">&amp;</span> <span class="p">(</span><span class="n">metadata</span><span class="o">.</span><span class="n">type</span> <span class="o">==</span> <span class="n">crop</span><span class="p">)]</span>
            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">sampleGroupMeta</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span> <span class="k">continue</span>
            <span class="n">sampleAbundance</span> <span class="o">=</span> <span class="n">seqCounter</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
            <span class="n">samplePresence</span> <span class="o">=</span> <span class="n">seqCounter</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
            <span class="n">comFileName</span> <span class="o">=</span> <span class="s2">&quot;stats/combined/</span><span class="si">%s</span><span class="s2">_</span><span class="si">%s</span><span class="s2">.tsv&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">sampleGroupMeta</span><span class="o">.</span><span class="n">plot_name</span><span class="o">.</span><span class="n">unique</span><span class="p">()[</span><span class="mi">0</span><span class="p">],</span><span class="n">date</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;/&quot;</span><span class="p">,</span><span class="s2">&quot;_&quot;</span><span class="p">))</span>
            <span class="nb">print</span><span class="p">(</span><span class="n">comFileName</span><span class="p">)</span>
            <span class="n">outfile</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">comFileName</span><span class="p">,</span> <span class="s2">&quot;w&quot;</span><span class="p">)</span>
            <span class="n">nfiles</span> <span class="o">=</span> <span class="mi">4</span>
            <span class="k">for</span> <span class="n">fstaName</span> <span class="ow">in</span> <span class="n">sampleGroupMeta</span><span class="o">.</span><span class="n">index</span><span class="p">:</span>
                <span class="k">try</span><span class="p">:</span>
                    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="s2">&quot;stats/</span><span class="si">%s</span><span class="s2">.tsv&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">fstaName</span><span class="p">))</span> <span class="k">as</span> <span class="n">fh</span><span class="p">:</span>
                        <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">fh</span><span class="p">:</span>
                            <span class="n">rec</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">()</span>
                            <span class="n">sampleAbundance</span><span class="p">[</span><span class="n">rec</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span> <span class="o">+=</span> <span class="nb">int</span><span class="p">(</span><span class="n">rec</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>
                            <span class="n">samplePresence</span><span class="p">[</span><span class="n">rec</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span>  <span class="o">+=</span> <span class="nb">int</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">rec</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span><span class="o">&gt;</span><span class="mi">0</span><span class="p">)</span>
                <span class="k">except</span><span class="p">:</span>
                    <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;</span><span class="se">\t\t</span><span class="s2">&quot;</span><span class="p">,</span><span class="n">comFileName</span><span class="p">,</span><span class="s2">&quot;is missing file:&quot;</span><span class="p">,</span><span class="n">fstaName</span><span class="p">)</span>
                    <span class="n">missingStats</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">fstaName</span><span class="p">)</span>
                    <span class="n">nfiles</span><span class="o">-=</span><span class="mi">1</span>
                    
            <span class="n">contigCounter</span> <span class="o">=</span> <span class="mi">0</span>
            <span class="k">for</span> <span class="n">contName</span><span class="p">,</span><span class="n">presCount</span> <span class="ow">in</span> <span class="n">samplePresence</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
                <span class="n">contigCounter</span> <span class="o">+=</span> <span class="nb">int</span><span class="p">(</span><span class="n">presCount</span> <span class="o">&gt;=</span> <span class="mi">2</span><span class="p">)</span>
                <span class="n">outfile</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">&quot;</span><span class="si">%s</span><span class="se">\t</span><span class="si">%s</span><span class="se">\n</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">contName</span><span class="p">,</span><span class="nb">int</span><span class="p">(</span><span class="n">sampleAbundance</span><span class="p">[</span><span class="n">contName</span><span class="p">]</span><span class="o">/</span><span class="n">nfiles</span><span class="p">)))</span>
                <span class="n">combined_abundance</span><span class="p">[</span><span class="n">contName</span><span class="p">]</span> <span class="o">+=</span> <span class="nb">int</span><span class="p">(</span><span class="n">sampleAbundance</span><span class="p">[</span><span class="n">contName</span><span class="p">]</span><span class="o">/</span><span class="n">nfiles</span><span class="p">)</span>
            <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">,</span><span class="n">contigCounter</span><span class="p">,</span><span class="s2">&quot;Contigs Present&quot;</span><span class="p">)</span>
            <span class="n">outfile</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
<span class="n">dump</span><span class="p">(</span><span class="n">combined_abundance</span><span class="p">,</span><span class="nb">open</span><span class="p">(</span><span class="s2">&quot;pickles/combined_abundance.p&quot;</span><span class="p">,</span><span class="s2">&quot;wb&quot;</span><span class="p">))</span>
<span class="n">dump</span><span class="p">(</span><span class="n">missingStats</span><span class="p">,</span><span class="nb">open</span><span class="p">(</span><span class="s2">&quot;pickles/missingStats.p&quot;</span><span class="p">,</span><span class="s2">&quot;wb&quot;</span><span class="p">))</span>
</pre></div>

    </div>
</div>
</div>

  </div>
<div class="cell border-box-sizing text_cell rendered"><div class="inner_cell">
<div class="text_cell_render border-box-sizing rendered_html">
<h3><a id="pltao">Plot abundance and occupancy</a></h3>
</div>
</div>
</div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="c1"># Now that the files are combined, let&#39;s look at p/a and abundance</span>
<span class="n">fileNames</span> <span class="o">=</span> <span class="n">glob</span><span class="p">(</span><span class="s2">&quot;stats/combined/*.tsv&quot;</span><span class="p">)</span>
<span class="n">presAbs</span><span class="p">,</span><span class="n">abundance</span> <span class="o">=</span> <span class="p">{},{}</span>
<span class="k">for</span> <span class="n">fname</span> <span class="ow">in</span> <span class="n">fileNames</span><span class="p">:</span>
    <span class="nb">print</span><span class="p">(</span><span class="n">fname</span><span class="p">)</span>
    <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">open</span><span class="p">(</span><span class="n">fname</span><span class="p">):</span> 
        <span class="n">rec</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">()</span>
        <span class="k">try</span><span class="p">:</span><span class="n">presAbs</span><span class="p">[</span><span class="n">rec</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span> <span class="o">+=</span> <span class="nb">int</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">rec</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">)</span>
        <span class="k">except</span><span class="p">:</span><span class="n">presAbs</span><span class="p">[</span><span class="n">rec</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">rec</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">)</span>
        <span class="k">try</span><span class="p">:</span><span class="n">abundance</span><span class="p">[</span><span class="n">rec</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span> <span class="o">+=</span> <span class="nb">int</span><span class="p">(</span><span class="n">rec</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
        <span class="k">except</span><span class="p">:</span><span class="n">abundance</span><span class="p">[</span><span class="n">rec</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">rec</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>

<span class="n">dump</span><span class="p">(</span><span class="n">presAbs</span><span class="p">,</span><span class="nb">open</span><span class="p">(</span><span class="s2">&quot;presence_absence_combined.p&quot;</span><span class="p">,</span><span class="s2">&quot;wb&quot;</span><span class="p">))</span>    
<span class="n">dump</span><span class="p">(</span><span class="n">abundance</span><span class="p">,</span><span class="nb">open</span><span class="p">(</span><span class="s2">&quot;abundance_combined.p&quot;</span><span class="p">,</span><span class="s2">&quot;wb&quot;</span><span class="p">))</span>   
<span class="n">dist_pres</span> <span class="o">=</span> <span class="p">[]</span>
<span class="n">numSamples</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">fileNames</span><span class="p">))</span>
<span class="k">for</span> <span class="n">contig</span><span class="p">,</span> <span class="n">count</span> <span class="ow">in</span> <span class="n">presAbs</span><span class="o">.</span><span class="n">items</span><span class="p">():</span> <span class="n">dist_pres</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">count</span><span class="o">/</span><span class="nb">float</span><span class="p">(</span><span class="n">numSamples</span><span class="p">))</span>
<span class="n">plotter</span> <span class="o">=</span> <span class="n">Series</span><span class="p">(</span><span class="n">dist_pres</span><span class="p">)</span>
<span class="n">plotter</span><span class="o">.</span><span class="n">plot</span><span class="o">.</span><span class="n">hist</span><span class="p">();</span>
</pre></div>

    </div>
</div>
</div>

  </div>
<div class="cell border-box-sizing text_cell rendered"><div class="inner_cell">
<div class="text_cell_render border-box-sizing rendered_html">
<h3><a id="pltao">Abundance</a></h3>
</div>
</div>
</div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="c1"># combinedFiles = glob(&quot;stats/combined/filtered/*.tsv&quot;)</span>
<span class="c1"># presAbs = load(open(&quot;pickles/presence_absence_combined.p&quot;,&quot;rb&quot;))    </span>
<span class="c1"># abundance = load(open(&quot;pickles/abundance_combined.p&quot;,&quot;rb&quot;))   </span>
<span class="c1"># dist_pres = []</span>
<span class="c1"># numSamples = float(len(combinedFiles))</span>
<span class="c1"># for contig, count in presAbs.items(): dist_pres.append(count/float(numSamples))</span>
<span class="c1"># plotter = Series(dist_pres)</span>
<span class="n">ax</span> <span class="o">=</span> <span class="n">plotter</span><span class="o">.</span><span class="n">plot</span><span class="o">.</span><span class="n">hist</span><span class="p">()</span>  <span class="c1"># s is an instance of Series</span>
<span class="n">fig</span> <span class="o">=</span> <span class="n">ax</span><span class="o">.</span><span class="n">get_figure</span><span class="p">()</span>
<span class="n">fig</span><span class="o">.</span><span class="n">savefig</span><span class="p">(</span><span class="s1">&#39;figures/Abundance_combined.png&#39;</span><span class="p">)</span>
<span class="n">ax</span><span class="p">;</span>
</pre></div>

    </div>
</div>
</div>

  </div>
<div class="cell border-box-sizing text_cell rendered"><div class="inner_cell">
<div class="text_cell_render border-box-sizing rendered_html">
<h3><a id="OXA">Occupancy X Abundance</a></h3>
</div>
</div>
</div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="k">as</span> <span class="nn">plt</span>
<span class="n">xs</span><span class="p">,</span> <span class="n">ys</span> <span class="o">=</span><span class="p">[],</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span><span class="mi">1000</span><span class="p">):</span>
    <span class="n">xs</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">i</span><span class="o">/</span><span class="mf">1000.0</span><span class="p">)</span>
    <span class="n">ys</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">plotter</span><span class="p">[</span><span class="n">plotter</span> <span class="o">&gt;</span> <span class="n">i</span><span class="o">/</span><span class="mf">1000.0</span><span class="p">]))</span>
<span class="n">plt</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">xs</span><span class="p">,</span><span class="n">ys</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">xlabel</span><span class="p">(</span><span class="s1">&#39;Percent of samples&#39;</span><span class="p">,</span><span class="n">fontsize</span><span class="o">=</span><span class="mi">14</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">ylabel</span><span class="p">(</span><span class="s1">&#39;Rank Abundance&#39;</span><span class="p">,</span><span class="n">fontsize</span><span class="o">=</span><span class="mi">14</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">savefig</span><span class="p">(</span><span class="s2">&quot;figures/OccupencyAbundance.png&quot;</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">show</span><span class="p">()</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="k">as</span> <span class="nn">plt</span>
<span class="n">xs</span><span class="p">,</span> <span class="n">ys</span> <span class="o">=</span><span class="p">[],</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">contName</span> <span class="ow">in</span> <span class="n">presAbs</span><span class="p">:</span>
    <span class="n">ys</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">presAbs</span><span class="p">[</span><span class="n">contName</span><span class="p">]</span><span class="o">/</span><span class="n">numSamples</span><span class="p">)</span>
    <span class="n">xs</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">abundance</span><span class="p">[</span><span class="n">contName</span><span class="p">])</span>
<span class="n">plt</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">xs</span><span class="p">,</span><span class="n">ys</span><span class="p">,</span><span class="s1">&#39;ro&#39;</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">xlabel</span><span class="p">(</span><span class="s1">&#39;Abundance&#39;</span><span class="p">,</span><span class="n">fontsize</span><span class="o">=</span><span class="mi">14</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">ylabel</span><span class="p">(</span><span class="s1">&#39;% Presence&#39;</span><span class="p">,</span><span class="n">fontsize</span><span class="o">=</span><span class="mi">14</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">show</span><span class="p">()</span>
</pre></div>

    </div>
</div>
</div>

  </div>
<div class="cell border-box-sizing text_cell rendered"><div class="inner_cell">
<div class="text_cell_render border-box-sizing rendered_html">
<h2><a id="pltao">Filter the data by occupency and abundance</a></h2>
</div>
</div>
</div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">numSamples</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">fileNames</span><span class="p">))</span>
<span class="c1"># keeperContigs = set()</span>
<span class="c1"># for contig, count in presAbs.items(): </span>
<span class="c1">#     if count/float(numSamples) &gt;= .25: keeperContigs.add(contig)</span>
<span class="nb">print</span> <span class="p">(</span><span class="s2">&quot;Keeping </span><span class="si">%i</span><span class="s2"> contigs&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">keeperContigs</span><span class="p">)))</span>

<span class="n">fileNames</span> <span class="o">=</span> <span class="n">glob</span><span class="p">(</span><span class="s2">&quot;stats/combined/*.tsv&quot;</span><span class="p">)</span>
<span class="n">presAbs</span><span class="p">,</span><span class="n">abundance</span> <span class="o">=</span> <span class="p">{},{}</span>

<span class="nb">print</span><span class="p">(</span><span class="s2">&quot;</span><span class="si">%i</span><span class="s2"> combined samples&quot;</span><span class="o">%</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">numSamples</span><span class="p">)))</span>
<span class="n">counter</span><span class="o">=</span><span class="mi">0</span>
<span class="k">for</span> <span class="n">fname</span> <span class="ow">in</span> <span class="n">fileNames</span><span class="p">:</span>
    <span class="n">counter</span> <span class="o">+=</span> <span class="mi">1</span>
    <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;</span><span class="si">%i</span><span class="s2">.&quot;</span> <span class="o">%</span> <span class="n">counter</span><span class="p">,</span><span class="n">fname</span><span class="p">)</span>
    <span class="n">ffh</span> <span class="o">=</span>  <span class="nb">open</span><span class="p">(</span><span class="n">fname</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;stats/combined/&quot;</span><span class="p">,</span><span class="s2">&quot;stats/combined/filtered/&quot;</span><span class="p">),</span><span class="s2">&quot;w&quot;</span><span class="p">)</span>
    <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">open</span><span class="p">(</span><span class="n">fname</span><span class="p">):</span> 
        <span class="n">rec</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">()</span>
        <span class="k">if</span> <span class="n">rec</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">in</span> <span class="n">keeperContigs</span><span class="p">:</span> 
            <span class="n">ffh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">&quot;</span><span class="si">%s</span><span class="se">\t</span><span class="si">%s</span><span class="se">\n</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">rec</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span><span class="n">rec</span><span class="p">[</span><span class="mi">1</span><span class="p">]))</span>
            <span class="k">try</span><span class="p">:</span><span class="n">presAbs</span><span class="p">[</span><span class="n">rec</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span>     <span class="o">+=</span> <span class="nb">int</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">rec</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">)</span>
            <span class="k">except</span><span class="p">:</span><span class="n">presAbs</span><span class="p">[</span><span class="n">rec</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span>   <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">rec</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">)</span>
            <span class="k">try</span><span class="p">:</span><span class="n">abundance</span><span class="p">[</span><span class="n">rec</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span>   <span class="o">+=</span> <span class="nb">int</span><span class="p">(</span><span class="n">rec</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
            <span class="k">except</span><span class="p">:</span><span class="n">abundance</span><span class="p">[</span><span class="n">rec</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">rec</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
    <span class="n">ffh</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
    
<span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="k">as</span> <span class="nn">plt</span>
<span class="n">xs</span><span class="p">,</span> <span class="n">ys</span> <span class="o">=</span><span class="p">[],</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">contName</span> <span class="ow">in</span> <span class="n">presAbs</span><span class="p">:</span>
    <span class="n">xs</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">presAbs</span><span class="p">[</span><span class="n">contName</span><span class="p">]</span><span class="o">/</span><span class="n">numSamples</span><span class="p">)</span>
    <span class="n">ys</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">abundance</span><span class="p">[</span><span class="n">contName</span><span class="p">])</span>
<span class="n">plt</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">xs</span><span class="p">,</span><span class="n">ys</span><span class="p">,</span><span class="s1">&#39;ro&#39;</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">xlabel</span><span class="p">(</span><span class="s1">&#39;Percent Abundance&#39;</span><span class="p">,</span><span class="n">fontsize</span><span class="o">=</span><span class="mi">14</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">ylabel</span><span class="p">(</span><span class="s1">&#39;Abundance&#39;</span><span class="p">,</span><span class="n">fontsize</span><span class="o">=</span><span class="mi">14</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">show</span><span class="p">()</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">fileNames</span> <span class="o">=</span> <span class="n">glob</span><span class="p">(</span><span class="s2">&quot;stats/combined/filtered/*.tsv&quot;</span><span class="p">)</span>
<span class="n">allCounts</span> <span class="o">=</span> <span class="p">{}</span>
<span class="n">counter</span><span class="o">=</span><span class="mi">0</span>
<span class="k">for</span> <span class="n">fname</span> <span class="ow">in</span> <span class="n">fileNames</span><span class="p">:</span>
    <span class="n">sampleName</span> <span class="o">=</span> <span class="n">fname</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;stats/combined/filtered/&quot;</span><span class="p">,</span><span class="s2">&quot;&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;.tsv&quot;</span><span class="p">,</span><span class="s2">&quot;&quot;</span><span class="p">)</span>
    <span class="n">allCounts</span><span class="p">[</span><span class="n">sampleName</span><span class="p">]</span><span class="o">=</span><span class="p">{}</span>
    <span class="n">counter</span><span class="o">+=</span><span class="mi">1</span>
    <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;</span><span class="si">%i</span><span class="s2">. </span><span class="si">%s</span><span class="s2">&quot;</span><span class="o">%</span><span class="p">(</span><span class="n">counter</span><span class="p">,</span><span class="n">sampleName</span><span class="p">))</span>
    <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">open</span><span class="p">(</span><span class="n">fname</span><span class="p">):</span>
        <span class="n">rec</span><span class="o">=</span><span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">()</span>
        <span class="n">allCounts</span><span class="p">[</span><span class="n">sampleName</span><span class="p">][</span><span class="n">rec</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span><span class="o">=</span><span class="nb">int</span><span class="p">(</span><span class="n">rec</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
<span class="n">dump</span><span class="p">(</span><span class="n">allCounts</span><span class="p">,</span><span class="nb">open</span><span class="p">(</span><span class="s2">&quot;pickles/sampleDict.p&quot;</span><span class="p">,</span><span class="s2">&quot;wb&quot;</span><span class="p">))</span>    
</pre></div>

    </div>
</div>
</div>

  </div>
<div class="cell border-box-sizing text_cell rendered"><div class="inner_cell">
<div class="text_cell_render border-box-sizing rendered_html">
<h2><a id="nmds">NMDS</a></h2>
</div>
</div>
</div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">sampleOrder</span> <span class="o">=</span> <span class="p">{}</span>
<span class="n">counter</span> <span class="o">=</span> <span class="mi">0</span>
<span class="n">dates</span><span class="o">=</span><span class="n">metadata</span><span class="p">[[</span><span class="s2">&quot;sampling_date&quot;</span><span class="p">,</span><span class="s2">&quot;Date&quot;</span><span class="p">]]</span>
<span class="n">dates</span><span class="o">=</span><span class="n">dates</span><span class="o">.</span><span class="n">sort_values</span><span class="p">(</span><span class="n">by</span><span class="o">=</span><span class="s2">&quot;Date&quot;</span><span class="p">)</span>
<span class="n">dates</span><span class="o">=</span><span class="n">dates</span><span class="p">[</span><span class="s2">&quot;sampling_date&quot;</span><span class="p">]</span>
    
<span class="k">for</span> <span class="n">date</span> <span class="ow">in</span> <span class="n">dates</span><span class="o">.</span><span class="n">unique</span><span class="p">():</span>
    <span class="k">for</span> <span class="n">crop</span> <span class="ow">in</span> <span class="nb">set</span><span class="p">(</span><span class="n">metadata</span><span class="o">.</span><span class="n">type</span><span class="p">):</span>
        <span class="k">for</span> <span class="n">treatment</span> <span class="ow">in</span> <span class="nb">set</span><span class="p">(</span><span class="n">metadata</span><span class="o">.</span><span class="n">treatment</span><span class="p">):</span>
            <span class="n">sampleGroupMeta</span> <span class="o">=</span> <span class="n">metadata</span><span class="o">.</span><span class="n">loc</span><span class="p">[(</span><span class="n">metadata</span><span class="o">.</span><span class="n">sampling_date</span><span class="o">==</span><span class="n">date</span><span class="p">)</span> <span class="o">&amp;</span> <span class="p">(</span><span class="n">metadata</span><span class="o">.</span><span class="n">treatment</span><span class="o">==</span><span class="n">treatment</span><span class="p">)</span> <span class="o">&amp;</span> <span class="p">(</span><span class="n">metadata</span><span class="o">.</span><span class="n">type</span> <span class="o">==</span> <span class="n">crop</span><span class="p">)]</span>
            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">sampleGroupMeta</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span> <span class="k">continue</span>
            <span class="n">idName</span> <span class="o">=</span> <span class="s2">&quot;</span><span class="si">%s</span><span class="s2">_</span><span class="si">%s</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">sampleGroupMeta</span><span class="o">.</span><span class="n">plot_name</span><span class="o">.</span><span class="n">unique</span><span class="p">()[</span><span class="mi">0</span><span class="p">],</span><span class="n">date</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;/&quot;</span><span class="p">,</span><span class="s2">&quot;_&quot;</span><span class="p">))</span>
            <span class="n">counter</span><span class="o">+=</span><span class="mi">1</span>
            <span class="n">sampleOrder</span><span class="p">[</span><span class="n">idName</span><span class="p">]</span> <span class="o">=</span> <span class="n">counter</span>

<span class="nb">print</span><span class="p">(</span><span class="s2">&quot;Loading sample counts&quot;</span><span class="p">)</span>
<span class="n">allCounts</span> <span class="o">=</span> <span class="n">load</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="s2">&quot;pickles/sampleDict.p&quot;</span><span class="p">,</span><span class="s2">&quot;rb&quot;</span><span class="p">))</span>
<span class="n">allCounts</span> <span class="o">=</span> <span class="n">DataFrame</span><span class="p">(</span><span class="n">allCounts</span><span class="p">)</span><span class="o">.</span><span class="n">transpose</span><span class="p">()</span>
<span class="n">allCounts</span><span class="p">[</span><span class="s1">&#39;Rank&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">allCounts</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">to_series</span><span class="p">()</span><span class="o">.</span><span class="n">map</span><span class="p">(</span><span class="n">sampleOrder</span><span class="p">)</span>
<span class="n">allCounts</span><span class="o">.</span><span class="n">sort_values</span><span class="p">(</span><span class="s1">&#39;Rank&#39;</span><span class="p">,</span><span class="n">inplace</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
<span class="n">allCounts</span><span class="o">.</span><span class="n">drop</span><span class="p">(</span><span class="s1">&#39;Rank&#39;</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="n">inplace</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
<span class="n">allCounts</span><span class="o">.</span><span class="n">head</span><span class="p">()</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">seed</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">RandomState</span><span class="p">(</span><span class="n">seed</span><span class="o">=</span><span class="mi">3</span><span class="p">)</span>
<span class="n">allCounts_matrix</span> <span class="o">=</span> <span class="n">allCounts</span><span class="o">.</span><span class="n">as_matrix</span><span class="p">()</span>
<span class="n">similarities</span> <span class="o">=</span> <span class="n">euclidean_distances</span><span class="p">(</span><span class="n">allCounts_matrix</span><span class="p">)</span>

<span class="n">nsamples</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">allCounts</span><span class="p">)</span>
<span class="n">mds</span> <span class="o">=</span> <span class="n">manifold</span><span class="o">.</span><span class="n">MDS</span><span class="p">(</span><span class="n">n_components</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span> <span class="n">max_iter</span><span class="o">=</span><span class="mi">3000</span><span class="p">,</span> <span class="n">eps</span><span class="o">=</span><span class="mf">1e-9</span><span class="p">,</span> <span class="n">random_state</span><span class="o">=</span><span class="n">seed</span><span class="p">,</span> <span class="n">dissimilarity</span><span class="o">=</span><span class="s2">&quot;precomputed&quot;</span><span class="p">,</span> <span class="n">n_jobs</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
<span class="n">pos</span> <span class="o">=</span> <span class="n">mds</span><span class="o">.</span><span class="n">fit</span><span class="p">(</span><span class="n">similarities</span><span class="p">)</span><span class="o">.</span><span class="n">embedding_</span>
<span class="n">nmds</span> <span class="o">=</span> <span class="n">manifold</span><span class="o">.</span><span class="n">MDS</span><span class="p">(</span><span class="n">n_components</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span> <span class="n">metric</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">max_iter</span><span class="o">=</span><span class="mi">3000</span><span class="p">,</span> <span class="n">eps</span><span class="o">=</span><span class="mf">1e-12</span><span class="p">,</span> <span class="n">dissimilarity</span><span class="o">=</span><span class="s2">&quot;precomputed&quot;</span><span class="p">,</span> <span class="n">random_state</span><span class="o">=</span><span class="n">seed</span><span class="p">,</span> <span class="n">n_jobs</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">n_init</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
<span class="n">npos</span> <span class="o">=</span> <span class="n">nmds</span><span class="o">.</span><span class="n">fit_transform</span><span class="p">(</span><span class="n">similarities</span><span class="p">,</span> <span class="n">init</span><span class="o">=</span><span class="n">pos</span><span class="p">)</span>

<span class="n">fig</span> <span class="o">=</span> <span class="n">plt</span><span class="o">.</span><span class="n">figure</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span>
<span class="n">ax</span> <span class="o">=</span> <span class="n">plt</span><span class="o">.</span><span class="n">axes</span><span class="p">([</span><span class="mf">0.</span><span class="p">,</span> <span class="mf">0.</span><span class="p">,</span> <span class="mf">1.5</span><span class="p">,</span> <span class="mf">1.95</span><span class="p">])</span>
<span class="n">s</span> <span class="o">=</span> <span class="mi">100</span>
<span class="n">counter</span> <span class="o">=</span> <span class="mi">0</span>
<span class="n">group</span> <span class="o">=</span> <span class="mi">0</span>
<span class="n">totalGroups</span> <span class="o">=</span> <span class="n">nsamples</span><span class="o">/</span><span class="mi">4</span>
<span class="n">l1s</span><span class="p">,</span> <span class="n">l2s</span> <span class="o">=</span> <span class="p">[],</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">date</span> <span class="ow">in</span> <span class="n">dates</span><span class="o">.</span><span class="n">unique</span><span class="p">():</span>
    <span class="n">group</span><span class="o">+=</span><span class="mi">1</span>
    <span class="n">l1s</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s2">&quot;SG-Fert &quot;</span><span class="o">+</span><span class="n">date</span><span class="p">)</span>
    <span class="n">plt</span><span class="o">.</span><span class="n">scatter</span><span class="p">(</span><span class="n">npos</span><span class="p">[</span><span class="n">counter</span><span class="p">:</span><span class="n">counter</span><span class="o">+</span><span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">],</span> <span class="n">npos</span><span class="p">[</span><span class="n">counter</span><span class="p">:</span><span class="n">counter</span><span class="o">+</span><span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">],</span> <span class="n">color</span><span class="o">=</span><span class="n">scolor</span><span class="p">(</span><span class="n">group</span><span class="p">,</span><span class="n">totalGroups</span><span class="p">,</span><span class="kc">True</span><span class="p">),</span> <span class="n">s</span><span class="o">=</span><span class="n">s</span><span class="p">,</span> <span class="n">lw</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">label</span><span class="o">=</span><span class="s2">&quot;SG-Fert &quot;</span><span class="o">+</span><span class="n">date</span><span class="p">,</span><span class="n">marker</span><span class="o">=</span><span class="s2">&quot;^&quot;</span><span class="p">)</span>
    <span class="n">counter</span><span class="o">+=</span><span class="mi">1</span>
    <span class="n">l1s</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s2">&quot;SG-NF &quot;</span><span class="o">+</span><span class="n">date</span><span class="p">)</span>
    <span class="n">plt</span><span class="o">.</span><span class="n">scatter</span><span class="p">(</span><span class="n">npos</span><span class="p">[</span><span class="n">counter</span><span class="p">:</span><span class="n">counter</span><span class="o">+</span><span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">],</span> <span class="n">npos</span><span class="p">[</span><span class="n">counter</span><span class="p">:</span><span class="n">counter</span><span class="o">+</span><span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">],</span> <span class="n">color</span><span class="o">=</span><span class="n">scolor</span><span class="p">(</span><span class="n">group</span><span class="p">,</span><span class="n">totalGroups</span><span class="p">,</span><span class="kc">True</span><span class="p">),</span> <span class="n">s</span><span class="o">=</span><span class="n">s</span><span class="p">,</span> <span class="n">lw</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">label</span><span class="o">=</span><span class="s2">&quot;SG-NF &quot;</span><span class="o">+</span><span class="n">date</span><span class="p">,</span><span class="n">marker</span><span class="o">=</span><span class="s2">&quot;v&quot;</span><span class="p">)</span>
    <span class="n">counter</span><span class="o">+=</span><span class="mi">1</span>
    <span class="n">l2s</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s2">&quot;MC-Fert &quot;</span><span class="o">+</span><span class="n">date</span><span class="p">)</span>
    <span class="n">plt</span><span class="o">.</span><span class="n">scatter</span><span class="p">(</span><span class="n">npos</span><span class="p">[</span><span class="n">counter</span><span class="p">:</span><span class="n">counter</span><span class="o">+</span><span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">],</span> <span class="n">npos</span><span class="p">[</span><span class="n">counter</span><span class="p">:</span><span class="n">counter</span><span class="o">+</span><span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">],</span> <span class="n">color</span><span class="o">=</span><span class="n">scolor</span><span class="p">(</span><span class="n">group</span><span class="p">,</span><span class="n">totalGroups</span><span class="p">,</span><span class="kc">False</span><span class="p">),</span> <span class="n">s</span><span class="o">=</span><span class="n">s</span><span class="p">,</span> <span class="n">lw</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">label</span><span class="o">=</span><span class="s2">&quot;MC-Fert &quot;</span><span class="o">+</span><span class="n">date</span><span class="p">,</span><span class="n">marker</span><span class="o">=</span><span class="s2">&quot;p&quot;</span><span class="p">)</span>
    <span class="n">counter</span><span class="o">+=</span><span class="mi">1</span>
    <span class="n">l2s</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s2">&quot;MC-NF &quot;</span><span class="o">+</span><span class="n">date</span><span class="p">)</span>
    <span class="n">plt</span><span class="o">.</span><span class="n">scatter</span><span class="p">(</span><span class="n">npos</span><span class="p">[</span><span class="n">counter</span><span class="p">:</span><span class="n">counter</span><span class="o">+</span><span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">],</span> <span class="n">npos</span><span class="p">[</span><span class="n">counter</span><span class="p">:</span><span class="n">counter</span><span class="o">+</span><span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">],</span> <span class="n">color</span><span class="o">=</span><span class="n">scolor</span><span class="p">(</span><span class="n">group</span><span class="p">,</span><span class="n">totalGroups</span><span class="p">,</span><span class="kc">False</span><span class="p">),</span> <span class="n">s</span><span class="o">=</span><span class="n">s</span><span class="p">,</span> <span class="n">lw</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">label</span><span class="o">=</span><span class="s2">&quot;MC-NF &quot;</span><span class="o">+</span><span class="n">date</span><span class="p">,</span><span class="n">marker</span><span class="o">=</span><span class="s2">&quot;H&quot;</span><span class="p">)</span>
    <span class="n">counter</span><span class="o">+=</span><span class="mi">1</span>

<span class="n">handles</span><span class="p">,</span> <span class="n">labels</span> <span class="o">=</span> <span class="n">ax</span><span class="o">.</span><span class="n">get_legend_handles_labels</span><span class="p">()</span>
<span class="c1"># sort both labels and handles by labels</span>
<span class="c1"># labels, handles = zip(*sorted(zip(labels, handles), key=lambda t: t[0]))</span>
<span class="c1"># ax.legend(handles, labels)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">legend</span><span class="p">(</span><span class="n">handles</span><span class="p">,</span> <span class="n">labels</span><span class="p">,</span><span class="n">scatterpoints</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">loc</span><span class="o">=</span><span class="s1">&#39;best&#39;</span><span class="p">,</span> <span class="n">shadow</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">title</span><span class="p">(</span><span class="s2">&quot;Switchgrass(SG) and Miscanthus(MC) Fertilized(Fert) &amp; Not Ferilized(NF) NMDS&quot;</span><span class="p">)</span>
<span class="c1"># plt.tight_layout()</span>
<span class="n">plt</span><span class="o">.</span><span class="n">savefig</span><span class="p">(</span><span class="s2">&quot;figures/AllCombinedNMDS.png&quot;</span><span class="p">,</span><span class="n">bbox_inches</span><span class="o">=</span><span class="s1">&#39;tight&#39;</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">show</span><span class="p">()</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">g6Data</span><span class="p">,</span> <span class="n">g5Data</span> <span class="o">=</span> <span class="p">[],[]</span>
<span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">allCounts</span><span class="o">.</span><span class="n">index</span><span class="p">:</span>
    <span class="k">if</span> <span class="n">key</span><span class="p">[:</span><span class="mi">2</span><span class="p">]</span> <span class="o">==</span> <span class="s2">&quot;G5&quot;</span><span class="p">:</span> <span class="n">g5Data</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">key</span><span class="p">)</span>
    <span class="k">else</span><span class="p">:</span> <span class="n">g6Data</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">key</span><span class="p">)</span>
<span class="n">g5Data</span> <span class="o">=</span> <span class="n">allCounts</span><span class="o">.</span><span class="n">drop</span><span class="p">(</span><span class="n">g5Data</span><span class="p">)</span>
<span class="n">g6Data</span> <span class="o">=</span> <span class="n">allCounts</span><span class="o">.</span><span class="n">drop</span><span class="p">(</span><span class="n">g6Data</span><span class="p">)</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">g5Data_matrix</span> <span class="o">=</span> <span class="n">g5Data</span><span class="o">.</span><span class="n">as_matrix</span><span class="p">()</span>
<span class="n">similarities</span> <span class="o">=</span> <span class="n">euclidean_distances</span><span class="p">(</span><span class="n">g5Data_matrix</span><span class="p">)</span>
<span class="n">nsamples</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">g5Data</span><span class="p">)</span>
<span class="n">mds</span> <span class="o">=</span> <span class="n">manifold</span><span class="o">.</span><span class="n">MDS</span><span class="p">(</span><span class="n">n_components</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span> <span class="n">max_iter</span><span class="o">=</span><span class="mi">3000</span><span class="p">,</span> <span class="n">eps</span><span class="o">=</span><span class="mf">1e-9</span><span class="p">,</span> <span class="n">random_state</span><span class="o">=</span><span class="n">seed</span><span class="p">,</span> <span class="n">dissimilarity</span><span class="o">=</span><span class="s2">&quot;precomputed&quot;</span><span class="p">,</span> <span class="n">n_jobs</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
<span class="n">pos</span> <span class="o">=</span> <span class="n">mds</span><span class="o">.</span><span class="n">fit</span><span class="p">(</span><span class="n">similarities</span><span class="p">)</span><span class="o">.</span><span class="n">embedding_</span>
<span class="n">nmds</span> <span class="o">=</span> <span class="n">manifold</span><span class="o">.</span><span class="n">MDS</span><span class="p">(</span><span class="n">n_components</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span> <span class="n">metric</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">max_iter</span><span class="o">=</span><span class="mi">3000</span><span class="p">,</span> <span class="n">eps</span><span class="o">=</span><span class="mf">1e-12</span><span class="p">,</span> <span class="n">dissimilarity</span><span class="o">=</span><span class="s2">&quot;precomputed&quot;</span><span class="p">,</span> <span class="n">random_state</span><span class="o">=</span><span class="n">seed</span><span class="p">,</span> <span class="n">n_jobs</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">n_init</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
<span class="n">npos</span> <span class="o">=</span> <span class="n">nmds</span><span class="o">.</span><span class="n">fit_transform</span><span class="p">(</span><span class="n">similarities</span><span class="p">,</span> <span class="n">init</span><span class="o">=</span><span class="n">pos</span><span class="p">)</span>

<span class="n">fig</span> <span class="o">=</span> <span class="n">plt</span><span class="o">.</span><span class="n">figure</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span>
<span class="n">ax</span> <span class="o">=</span> <span class="n">plt</span><span class="o">.</span><span class="n">axes</span><span class="p">([</span><span class="mf">0.</span><span class="p">,</span> <span class="mf">0.</span><span class="p">,</span> <span class="mf">1.5</span><span class="p">,</span> <span class="mf">1.95</span><span class="p">])</span>
<span class="n">s</span> <span class="o">=</span> <span class="mi">100</span>

<span class="k">for</span> <span class="n">index</span><span class="p">,</span> <span class="n">sample</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">g5Data</span><span class="o">.</span><span class="n">index</span><span class="p">):</span>
    <span class="n">species</span> <span class="o">=</span> <span class="s2">&quot;MC&quot;</span><span class="p">;</span> 
    <span class="k">if</span> <span class="n">sortedmeta</span><span class="p">[</span><span class="n">sortedmeta</span><span class="o">.</span><span class="n">nucleic_acid_name</span> <span class="o">==</span> <span class="n">sample</span><span class="p">]</span><span class="o">.</span><span class="n">treatment</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s2">&quot;nitrogen free&quot;</span><span class="p">:</span> 
        <span class="n">treatment</span> <span class="o">=</span> <span class="s2">&quot;NF&quot;</span>
        <span class="n">marker</span> <span class="o">=</span> <span class="s1">&#39;p&#39;</span>
    <span class="k">else</span><span class="p">:</span> 
        <span class="n">treatment</span> <span class="o">=</span> <span class="s2">&quot;Fert&quot;</span>
        <span class="n">marker</span><span class="o">=</span> <span class="s2">&quot;s&quot;</span>
            
    <span class="n">lbl</span> <span class="o">=</span> <span class="s2">&quot;</span><span class="si">%s</span><span class="s2">_</span><span class="si">%s</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">species</span><span class="p">,</span><span class="n">treatment</span><span class="p">)</span>
    <span class="n">plt</span><span class="o">.</span><span class="n">scatter</span><span class="p">(</span><span class="n">npos</span><span class="p">[</span><span class="n">index</span><span class="p">:</span><span class="n">index</span><span class="o">+</span><span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">],</span> <span class="n">npos</span><span class="p">[</span><span class="n">index</span><span class="p">:</span><span class="n">index</span><span class="o">+</span><span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">],</span> <span class="n">color</span><span class="o">=</span><span class="n">scolor</span><span class="p">(</span><span class="n">index</span><span class="o">+</span><span class="mi">71</span><span class="p">,</span><span class="mi">72</span><span class="p">,</span><span class="n">species</span> <span class="o">==</span> <span class="s2">&quot;SG&quot;</span><span class="p">),</span> <span class="n">s</span><span class="o">=</span><span class="n">s</span><span class="p">,</span> <span class="n">lw</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">label</span><span class="o">=</span><span class="n">lbl</span><span class="p">,</span><span class="n">marker</span><span class="o">=</span><span class="n">marker</span><span class="p">)</span>

<span class="c1">#plt.legend(scatterpoints=1, loc=&#39;best&#39;, shadow=False)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">title</span><span class="p">(</span><span class="s2">&quot;Miscanthus (Fert) and Not Ferilized (NF)&quot;</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">savefig</span><span class="p">(</span><span class="s2">&quot;figures/Miscanthus_NMDS_genes.png&quot;</span><span class="p">,</span> <span class="n">bbox_inches</span><span class="o">=</span><span class="s1">&#39;tight&#39;</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">show</span><span class="p">()</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">g6Data_matrix</span> <span class="o">=</span> <span class="n">g6Data</span><span class="o">.</span><span class="n">as_matrix</span><span class="p">()</span>
<span class="n">similarities</span> <span class="o">=</span> <span class="n">euclidean_distances</span><span class="p">(</span><span class="n">g6Data_matrix</span><span class="p">)</span>
<span class="n">nsamples</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">g6Data</span><span class="p">)</span>
<span class="n">mds</span> <span class="o">=</span> <span class="n">manifold</span><span class="o">.</span><span class="n">MDS</span><span class="p">(</span><span class="n">n_components</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span> <span class="n">max_iter</span><span class="o">=</span><span class="mi">3000</span><span class="p">,</span> <span class="n">eps</span><span class="o">=</span><span class="mf">1e-9</span><span class="p">,</span> <span class="n">random_state</span><span class="o">=</span><span class="n">seed</span><span class="p">,</span> <span class="n">dissimilarity</span><span class="o">=</span><span class="s2">&quot;precomputed&quot;</span><span class="p">,</span> <span class="n">n_jobs</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
<span class="n">pos</span> <span class="o">=</span> <span class="n">mds</span><span class="o">.</span><span class="n">fit</span><span class="p">(</span><span class="n">similarities</span><span class="p">)</span><span class="o">.</span><span class="n">embedding_</span>
<span class="n">nmds</span> <span class="o">=</span> <span class="n">manifold</span><span class="o">.</span><span class="n">MDS</span><span class="p">(</span><span class="n">n_components</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span> <span class="n">metric</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">max_iter</span><span class="o">=</span><span class="mi">3000</span><span class="p">,</span> <span class="n">eps</span><span class="o">=</span><span class="mf">1e-12</span><span class="p">,</span> <span class="n">dissimilarity</span><span class="o">=</span><span class="s2">&quot;precomputed&quot;</span><span class="p">,</span> <span class="n">random_state</span><span class="o">=</span><span class="n">seed</span><span class="p">,</span> <span class="n">n_jobs</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">n_init</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
<span class="n">npos</span> <span class="o">=</span> <span class="n">nmds</span><span class="o">.</span><span class="n">fit_transform</span><span class="p">(</span><span class="n">similarities</span><span class="p">,</span> <span class="n">init</span><span class="o">=</span><span class="n">pos</span><span class="p">)</span>

<span class="n">fig</span> <span class="o">=</span> <span class="n">plt</span><span class="o">.</span><span class="n">figure</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span>
<span class="n">ax</span> <span class="o">=</span> <span class="n">plt</span><span class="o">.</span><span class="n">axes</span><span class="p">([</span><span class="mf">0.</span><span class="p">,</span> <span class="mf">0.</span><span class="p">,</span> <span class="mf">1.5</span><span class="p">,</span> <span class="mf">1.5</span><span class="p">])</span>
<span class="n">s</span> <span class="o">=</span> <span class="mi">100</span>
<span class="n">counter</span> <span class="o">=</span> <span class="mi">0</span>
<span class="n">group</span><span class="o">=</span><span class="mi">0</span>
<span class="k">for</span> <span class="n">index</span><span class="p">,</span> <span class="n">sample</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">g6Data</span><span class="o">.</span><span class="n">index</span><span class="p">):</span>
    <span class="n">species</span> <span class="o">=</span> <span class="s2">&quot;SG&quot;</span><span class="p">;</span> 
    <span class="k">if</span> <span class="n">sortedmeta</span><span class="p">[</span><span class="n">sortedmeta</span><span class="o">.</span><span class="n">nucleic_acid_name</span> <span class="o">==</span> <span class="n">sample</span><span class="p">]</span><span class="o">.</span><span class="n">treatment</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s2">&quot;nitrogen free&quot;</span><span class="p">:</span> 
        <span class="n">treatment</span> <span class="o">=</span> <span class="s2">&quot;NF&quot;</span>
        <span class="n">marker</span> <span class="o">=</span> <span class="s1">&#39;^&#39;</span>
    <span class="k">else</span><span class="p">:</span> 
        <span class="n">treatment</span> <span class="o">=</span> <span class="s2">&quot;Fert&quot;</span>
        <span class="n">marker</span><span class="o">=</span> <span class="s2">&quot;v&quot;</span>   
    <span class="n">lbl</span> <span class="o">=</span> <span class="s2">&quot;</span><span class="si">%s</span><span class="s2">_</span><span class="si">%s</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">species</span><span class="p">,</span><span class="n">treatment</span><span class="p">)</span>
    <span class="n">plt</span><span class="o">.</span><span class="n">scatter</span><span class="p">(</span><span class="n">npos</span><span class="p">[</span><span class="n">index</span><span class="p">:</span><span class="n">index</span><span class="o">+</span><span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">],</span> <span class="n">npos</span><span class="p">[</span><span class="n">index</span><span class="p">:</span><span class="n">index</span><span class="o">+</span><span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">],</span> <span class="n">color</span><span class="o">=</span><span class="n">scolor</span><span class="p">(</span><span class="n">index</span><span class="p">,</span><span class="mi">72</span><span class="p">,</span><span class="n">species</span> <span class="o">==</span> <span class="s2">&quot;SG&quot;</span><span class="p">),</span> <span class="n">s</span><span class="o">=</span><span class="n">s</span><span class="p">,</span> <span class="n">lw</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">label</span><span class="o">=</span><span class="n">lbl</span><span class="p">,</span><span class="n">marker</span><span class="o">=</span><span class="n">marker</span><span class="p">)</span>

<span class="c1">#plt.legend(scatterpoints=1, loc=&#39;best&#39;, shadow=False)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">title</span><span class="p">(</span><span class="s2">&quot;Switchgrass Fertilized (Fert) and Not Ferilized (NF)&quot;</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">savefig</span><span class="p">(</span><span class="s2">&quot;figures/Switchgrass_NMDS_genes.png&quot;</span><span class="p">,</span> <span class="n">bbox_inches</span><span class="o">=</span><span class="s1">&#39;tight&#39;</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">show</span><span class="p">()</span>
</pre></div>

    </div>
</div>
</div>

  </div>
<div class="cell border-box-sizing text_cell rendered"><div class="inner_cell">
<div class="text_cell_render border-box-sizing rendered_html">
<h1><a id="metaT">Function Analysis</a></h1><p><a href="#meta">Home</a></p>

</div>
</div>
</div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">KO_Levels</span> <span class="o">=</span> <span class="n">DataFrame</span><span class="o">.</span><span class="n">from_csv</span><span class="p">(</span><span class="s2">&quot;annotations/KO_Levels.tsv&quot;</span><span class="p">,</span><span class="n">sep</span><span class="o">=</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
<span class="n">KO_Levels</span><span class="p">[</span><span class="s1">&#39;Level1&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">KO_Levels</span><span class="p">[</span><span class="s1">&#39;Level1&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">apply</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="nb">str</span><span class="p">(</span><span class="n">x</span><span class="p">)</span><span class="o">.</span><span class="n">zfill</span><span class="p">(</span><span class="mi">5</span><span class="p">))</span>
<span class="n">KO_Levels</span><span class="p">[</span><span class="s1">&#39;Level2&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">KO_Levels</span><span class="p">[</span><span class="s1">&#39;Level2&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">apply</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="nb">str</span><span class="p">(</span><span class="n">x</span><span class="p">)</span><span class="o">.</span><span class="n">zfill</span><span class="p">(</span><span class="mi">5</span><span class="p">))</span>
<span class="n">KO_Levels</span><span class="p">[</span><span class="s1">&#39;Level3&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">KO_Levels</span><span class="p">[</span><span class="s1">&#39;Level3&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">apply</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="nb">str</span><span class="p">(</span><span class="n">x</span><span class="p">)</span><span class="o">.</span><span class="n">zfill</span><span class="p">(</span><span class="mi">5</span><span class="p">))</span>
<span class="n">KO_Levels</span><span class="o">.</span><span class="n">head</span><span class="p">()</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">contigKOs</span> <span class="o">=</span> <span class="p">{}</span>
<span class="n">koContigs</span> <span class="o">=</span> <span class="p">{}</span>
<span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">open</span><span class="p">(</span><span class="s2">&quot;annotations/KEGG_tools_out/diamondAnnotations_0_KOtable.txt&quot;</span><span class="p">):</span>
    <span class="n">rec</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
    <span class="k">try</span><span class="p">:</span> <span class="n">contigKOs</span><span class="p">[</span><span class="n">rec</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">rec</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>
    <span class="k">except</span><span class="p">:</span> <span class="n">contigKOs</span><span class="p">[</span><span class="n">rec</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span> <span class="o">=</span> <span class="nb">set</span><span class="p">([</span><span class="n">rec</span><span class="p">[</span><span class="mi">2</span><span class="p">]])</span>
    <span class="k">try</span><span class="p">:</span> <span class="n">koContigs</span><span class="p">[</span><span class="n">rec</span><span class="p">[</span><span class="mi">2</span><span class="p">]]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">rec</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
    <span class="k">except</span><span class="p">:</span> <span class="n">koContigs</span><span class="p">[</span><span class="n">rec</span><span class="p">[</span><span class="mi">2</span><span class="p">]]</span> <span class="o">=</span> <span class="nb">set</span><span class="p">([</span><span class="n">rec</span><span class="p">[</span><span class="mi">0</span><span class="p">]])</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">allCounts</span> <span class="o">=</span> <span class="n">load</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="s2">&quot;pickles/allCounts_genes.p&quot;</span><span class="p">,</span><span class="s2">&quot;rb&quot;</span><span class="p">))</span> 
<span class="n">ko_mapper</span> <span class="o">=</span> <span class="n">load</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="s2">&quot;pickles/koMap.p&quot;</span><span class="p">,</span><span class="s2">&quot;rb&quot;</span><span class="p">))</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="kn">from</span> <span class="nn">numpy</span> <span class="k">import</span> <span class="n">log2</span>
<span class="n">levels</span> <span class="o">=</span> <span class="n">KO_Levels</span><span class="o">.</span><span class="n">Level1</span><span class="o">.</span><span class="n">unique</span><span class="p">()</span>
<span class="n">Level3DF</span> <span class="o">=</span> <span class="n">DataFrame</span><span class="p">(</span><span class="n">index</span><span class="o">=</span><span class="n">levels</span><span class="p">,</span> <span class="n">columns</span><span class="o">=</span><span class="n">allCounts</span><span class="o">.</span><span class="n">columns</span><span class="p">)</span>
<span class="n">Level3DF</span> <span class="o">=</span> <span class="n">Level3DF</span><span class="o">.</span><span class="n">fillna</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
<span class="k">for</span> <span class="n">level</span> <span class="ow">in</span> <span class="n">levels</span><span class="p">:</span>
    <span class="n">selectedKOs</span> <span class="o">=</span> <span class="n">KO_Levels</span><span class="p">[</span><span class="n">KO_Levels</span><span class="o">.</span><span class="n">Level1</span> <span class="o">==</span> <span class="n">level</span><span class="p">]</span>
    <span class="n">selectedContigs</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
    <span class="k">for</span> <span class="n">ko</span> <span class="ow">in</span> <span class="n">selectedKOs</span><span class="o">.</span><span class="n">index</span><span class="p">:</span> <span class="n">selectedContigs</span> <span class="o">=</span> <span class="n">selectedContigs</span><span class="o">.</span><span class="n">union</span><span class="p">(</span><span class="n">koContigs</span><span class="p">[</span><span class="n">ko</span><span class="p">])</span>
    <span class="n">selectedCounts</span> <span class="o">=</span> <span class="n">allCounts</span><span class="p">[</span><span class="n">allCounts</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">selectedContigs</span><span class="p">)]</span>
    <span class="n">countSums</span> <span class="o">=</span> <span class="n">selectedCounts</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
    <span class="n">countSums</span> <span class="o">=</span> <span class="n">readsForAllContigs</span>
    <span class="n">countSums</span> <span class="o">=</span> <span class="n">log2</span><span class="p">(</span><span class="n">countSums</span><span class="o">/</span><span class="n">readCounts</span><span class="p">[</span><span class="s2">&quot;TotalSampleReads&quot;</span><span class="p">])</span>
    <span class="n">Level3DF</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="n">level</span><span class="p">]</span> <span class="o">=</span> <span class="n">countSums</span>
<span class="n">Level3DF</span><span class="p">[</span><span class="s2">&quot;Description&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="n">Level3DF</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">to_series</span><span class="p">()</span><span class="o">.</span><span class="n">map</span><span class="p">(</span><span class="n">ko_mapper</span><span class="o">.</span><span class="n">descripts</span><span class="p">)</span>
<span class="n">cols</span> <span class="o">=</span> <span class="n">Level3DF</span><span class="o">.</span><span class="n">columns</span><span class="o">.</span><span class="n">tolist</span><span class="p">()</span>
<span class="n">cols</span> <span class="o">=</span> <span class="n">cols</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">:]</span> <span class="o">+</span> <span class="n">cols</span><span class="p">[:</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
<span class="n">Level3DF</span> <span class="o">=</span> <span class="n">Level3DF</span><span class="p">[</span><span class="n">cols</span><span class="p">]</span>
<span class="n">Level3DF</span><span class="o">=</span><span class="n">Level3DF</span><span class="o">.</span><span class="n">set_index</span><span class="p">(</span><span class="s1">&#39;Description&#39;</span><span class="p">)</span>
<span class="n">Level3DF</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span><span class="s2">&quot;annotations/Level1CountTable.tsv&quot;</span><span class="p">,</span><span class="n">sep</span><span class="o">=</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">readCounts</span> <span class="o">=</span> <span class="n">read_csv</span><span class="p">(</span><span class="s2">&quot;mapping/metaG/flagstats/multiqc_data/mqc_bowtie2_pe_plot_1.txt&quot;</span><span class="p">,</span><span class="n">sep</span><span class="o">=</span><span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">)</span>
<span class="n">readCounts</span><span class="p">[</span><span class="s2">&quot;TotalSampleReads&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="n">data</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
<span class="n">readCounts</span><span class="o">.</span><span class="n">set_index</span><span class="p">(</span><span class="s2">&quot;Sample&quot;</span><span class="p">,</span><span class="n">inplace</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="n">readCounts</span><span class="o">.</span><span class="n">head</span><span class="p">()</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="k">class</span> <span class="nc">KO_Mapper</span><span class="p">:</span>
    <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
        <span class="bp">self</span><span class="o">.</span><span class="n">koToMap</span> <span class="o">=</span> <span class="p">{}</span>
        <span class="bp">self</span><span class="o">.</span><span class="n">descripts</span> <span class="o">=</span> <span class="p">{}</span>
        <span class="bp">self</span><span class="o">.</span><span class="n">mapToKO</span> <span class="o">=</span> <span class="p">{}</span>
        <span class="bp">self</span><span class="o">.</span><span class="n">levelToMap</span> <span class="o">=</span> <span class="p">{}</span>
        <span class="bp">self</span><span class="o">.</span><span class="n">ko</span> <span class="o">=</span> <span class="s2">&quot;&quot;</span>
        <span class="bp">self</span><span class="o">.</span><span class="n">KEGG_URL</span> <span class="o">=</span> <span class="s2">&quot;https://www.kegg.jp/dbget-bin/www_bget?</span><span class="si">%s</span><span class="s2">&quot;</span>

    <span class="k">def</span> <span class="nf">setItem</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">level</span><span class="p">,</span> <span class="n">mapNum</span><span class="p">,</span> <span class="n">descrip</span><span class="p">):</span>
        <span class="c1"># print(self.ko, level, mapNum, descrip)</span>
        <span class="c1"># Map descriptions</span>
        <span class="bp">self</span><span class="o">.</span><span class="n">descripts</span><span class="p">[</span><span class="n">mapNum</span><span class="p">]</span> <span class="o">=</span> <span class="n">descrip</span>
        
        <span class="c1"># Map to KO</span>
        <span class="k">try</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">mapToKO</span><span class="p">[</span><span class="n">mapNum</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">ko</span><span class="p">)</span>
        <span class="k">except</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">mapToKO</span><span class="p">[</span><span class="n">mapNum</span><span class="p">]</span> <span class="o">=</span> <span class="nb">set</span><span class="p">([</span><span class="bp">self</span><span class="o">.</span><span class="n">ko</span><span class="p">])</span>
        
        <span class="c1"># KO to level to mapNum</span>
        <span class="k">try</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">koToMap</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">ko</span><span class="p">][</span><span class="n">level</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">mapNum</span><span class="p">)</span>
        <span class="k">except</span><span class="p">:</span> 
            <span class="k">try</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">koToMap</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">ko</span><span class="p">][</span><span class="n">level</span><span class="p">]</span> <span class="o">=</span> <span class="nb">set</span><span class="p">([</span><span class="n">mapNum</span><span class="p">])</span>
            <span class="k">except</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">koToMap</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">ko</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span> <span class="n">level</span><span class="p">:</span><span class="nb">set</span><span class="p">([</span><span class="n">mapNum</span><span class="p">])</span> <span class="p">}</span>
        
        <span class="c1"># Level to map</span>
        <span class="k">try</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">levelToMap</span><span class="p">[</span><span class="n">level</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">mapNum</span><span class="p">)</span>
        <span class="k">except</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">levelToMap</span><span class="p">[</span><span class="n">level</span><span class="p">]</span> <span class="o">=</span> <span class="nb">set</span><span class="p">([</span><span class="n">mapNum</span><span class="p">])</span>
                
    <span class="k">def</span> <span class="nf">_processKOInfo</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">koText</span><span class="p">):</span>
        <span class="n">rec</span> <span class="o">=</span> <span class="n">koText</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">)</span>
        <span class="k">while</span> <span class="s1">&#39;KEGG Orthology&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">rec</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="n">rec</span><span class="p">)</span><span class="o">&gt;</span><span class="mi">0</span><span class="p">:</span> <span class="n">rec</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="mi">1</span><span class="p">:]</span>
        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">rec</span><span class="p">)</span><span class="o">==</span><span class="mi">0</span><span class="p">:</span><span class="k">return</span>
        <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">rec</span><span class="p">[</span><span class="mi">1</span><span class="p">:]:</span>
            <span class="n">level</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\xa0</span><span class="s1">&#39;</span><span class="p">)</span>
            <span class="k">if</span> <span class="p">(</span><span class="n">level</span> <span class="o">==</span> <span class="mi">0</span><span class="p">)</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">ko</span> <span class="ow">in</span> <span class="nb">str</span><span class="p">(</span><span class="n">line</span><span class="p">):</span> <span class="k">break</span> <span class="c1">#Don&#39;t record any ribosome info</span>
            <span class="n">info</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\xa0</span><span class="s1">&#39;</span><span class="p">)</span>
            <span class="n">bIndex</span> <span class="o">=</span> <span class="n">info</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s2">&quot; &quot;</span><span class="p">)</span>
            <span class="bp">self</span><span class="o">.</span><span class="n">setItem</span><span class="p">(</span><span class="n">level</span><span class="p">,</span><span class="n">info</span><span class="p">[:</span><span class="n">bIndex</span><span class="p">],</span><span class="n">info</span><span class="p">[</span><span class="n">bIndex</span><span class="o">+</span><span class="mi">1</span><span class="p">:])</span>
    
    <span class="k">def</span> <span class="nf">mapKO</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">ko</span><span class="p">):</span>
        <span class="n">siteContent</span> <span class="o">=</span> <span class="n">BeautifulSoup</span><span class="p">(</span><span class="n">urlopen</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">KEGG_URL</span><span class="o">%</span><span class="p">(</span><span class="n">ko</span><span class="p">))</span><span class="o">.</span><span class="n">read</span><span class="p">(),</span><span class="n">features</span><span class="o">=</span><span class="s2">&quot;lxml&quot;</span><span class="p">)</span>
        <span class="bp">self</span><span class="o">.</span><span class="n">ko</span> <span class="o">=</span> <span class="n">ko</span>
        <span class="n">found</span> <span class="o">=</span> <span class="kc">False</span>
        <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">elm</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">siteContent</span><span class="o">.</span><span class="n">find_all</span><span class="p">(</span><span class="s2">&quot;td&quot;</span><span class="p">,</span> <span class="p">{</span><span class="s2">&quot;class&quot;</span><span class="p">:</span> <span class="s2">&quot;td41&quot;</span><span class="p">})):</span>
            <span class="k">if</span> <span class="s2">&quot;KEGG Orthology&quot;</span> <span class="ow">in</span> <span class="nb">str</span><span class="p">(</span><span class="n">elm</span><span class="o">.</span><span class="n">contents</span><span class="p">[</span><span class="mi">0</span><span class="p">]):</span>
                <span class="n">pathway</span> <span class="o">=</span> <span class="n">elm</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s2">&quot;nobr&quot;</span><span class="p">)</span>
                <span class="bp">self</span><span class="o">.</span><span class="n">_processKOInfo</span><span class="p">(</span><span class="n">pathway</span><span class="o">.</span><span class="n">text</span><span class="p">)</span>
                <span class="n">found</span> <span class="o">=</span> <span class="kc">True</span>
                <span class="k">break</span>
        <span class="k">if</span> <span class="ow">not</span> <span class="n">found</span><span class="p">:</span> 
            <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">elm</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">siteContent</span><span class="o">.</span><span class="n">find_all</span><span class="p">(</span><span class="s2">&quot;td&quot;</span><span class="p">,</span> <span class="p">{</span><span class="s2">&quot;class&quot;</span><span class="p">:</span> <span class="s2">&quot;td40&quot;</span><span class="p">})):</span>
                <span class="k">if</span> <span class="s2">&quot;KEGG Orthology&quot;</span> <span class="ow">in</span> <span class="nb">str</span><span class="p">(</span><span class="n">elm</span><span class="o">.</span><span class="n">contents</span><span class="p">[</span><span class="mi">0</span><span class="p">]):</span>
                    <span class="n">pathway</span> <span class="o">=</span> <span class="n">elm</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s2">&quot;nobr&quot;</span><span class="p">)</span>
                    <span class="bp">self</span><span class="o">.</span><span class="n">_processKOInfo</span><span class="p">(</span><span class="n">pathway</span><span class="o">.</span><span class="n">text</span><span class="p">)</span>
                    <span class="n">found</span> <span class="o">=</span> <span class="kc">True</span>
                    <span class="k">break</span>
        <span class="k">if</span> <span class="ow">not</span> <span class="n">found</span><span class="p">:</span> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">&quot;Unable to find &quot;</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">ko</span><span class="p">)</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">DataFrame</span><span class="o">.</span><span class="n">read_csv</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="c1">#A custom function to help us find the raw fastq files</span>
<span class="kn">from</span> <span class="nn">glob</span> <span class="k">import</span> <span class="n">glob</span>
<span class="n">rawFastqFiles</span> <span class="o">=</span> <span class="n">glob</span><span class="p">(</span><span class="s1">&#39;jgi_transfer/metaT_raw/*/Raw_Data/*&#39;</span><span class="p">)</span>

<span class="k">def</span> <span class="nf">lookupFSTQ</span><span class="p">(</span><span class="n">name</span><span class="p">,</span><span class="n">rawFastqFiles</span><span class="p">):</span>
    <span class="n">fastqName</span> <span class="o">=</span> <span class="s1">&#39;&#39;</span>
    <span class="n">found</span> <span class="o">=</span> <span class="kc">False</span>
    <span class="k">for</span> <span class="n">fastqName</span> <span class="ow">in</span> <span class="n">rawFastqFiles</span><span class="p">:</span>
        <span class="k">if</span> <span class="n">name</span> <span class="ow">in</span> <span class="n">fastqName</span><span class="p">:</span> 
            <span class="n">found</span> <span class="o">=</span> <span class="kc">True</span>
            <span class="k">break</span>
    <span class="k">if</span> <span class="n">found</span><span class="p">:</span>
        <span class="n">rawFastqFiles</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="n">fastqName</span><span class="p">)</span>
        <span class="k">return</span> <span class="n">fastqName</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span>%%bash
ls metadata
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="kn">from</span> <span class="nn">pandas</span> <span class="k">import</span> <span class="n">DataFrame</span><span class="p">,</span> <span class="n">to_datetime</span>
<span class="c1">#Collect Metadata</span>
<span class="n">metadata</span> <span class="o">=</span> <span class="n">DataFrame</span><span class="o">.</span><span class="n">from_csv</span><span class="p">(</span><span class="s2">&quot;metadata/GLBRC_MetaT_Metadata.tsv&quot;</span><span class="p">,</span><span class="n">sep</span><span class="o">=</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>

<span class="c1">#Change the data to only include things we are interested in and format a few columns</span>
<span class="n">metadata</span><span class="p">[</span><span class="s1">&#39;sampling_date&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">to_datetime</span><span class="p">(</span><span class="n">metadata</span><span class="o">.</span><span class="n">date</span><span class="p">)</span> <span class="c1">#Make date a format python can sort</span>
<span class="n">metadata</span><span class="o">.</span><span class="n">drop</span><span class="p">([</span><span class="s1">&#39;time&#39;</span><span class="p">,</span><span class="s1">&#39;air_temp_c&#39;</span><span class="p">,</span> <span class="s1">&#39;day&#39;</span><span class="p">,</span> <span class="s1">&#39;month&#39;</span><span class="p">,</span> <span class="s1">&#39;year&#39;</span><span class="p">,</span> <span class="s1">&#39;weather&#39;</span><span class="p">,</span> <span class="s1">&#39;notes&#39;</span><span class="p">,</span> <span class="s1">&#39;rep&#39;</span><span class="p">,</span> <span class="s1">&#39;date_of_extraction&#39;</span><span class="p">,</span> <span class="s1">&#39;nucleic_acid_type&#39;</span><span class="p">,</span> 
   <span class="s1">&#39;replicate_extraction&#39;</span><span class="p">,</span> <span class="s1">&#39;source&#39;</span><span class="p">,</span> <span class="s1">&#39;source_mass&#39;</span><span class="p">,</span> <span class="s1">&#39;extraction_method&#39;</span><span class="p">,</span> <span class="s1">&#39;elution_vol_ul&#39;</span><span class="p">,</span> <span class="s1">&#39;concentration_ng_per_ul&#39;</span><span class="p">,</span> 
   <span class="s1">&#39;ratio_260_280&#39;</span><span class="p">,</span> <span class="s1">&#39;conc_ng_per_g_source&#39;</span><span class="p">,</span> <span class="s1">&#39;extracted_by&#39;</span><span class="p">,</span> <span class="s1">&#39;sequencing_date&#39;</span><span class="p">,</span> <span class="s1">&#39;conc_sent_ng_per_ul&#39;</span><span class="p">,</span> <span class="s1">&#39;sequencing_type&#39;</span><span class="p">,</span> 
   <span class="s1">&#39;sequencing_facility&#39;</span><span class="p">,</span> <span class="s1">&#39;primers&#39;</span><span class="p">,</span> <span class="s1">&#39;submitted_for_sequencing&#39;</span><span class="p">,</span> <span class="s1">&#39;sequencing_successful&#39;</span><span class="p">,</span> <span class="s1">&#39;duplicate_submitted&#39;</span><span class="p">,</span> <span class="s1">&#39;dup_sequencing_name&#39;</span><span class="p">,</span> 
   <span class="s1">&#39;exclude_from_analysis&#39;</span><span class="p">,</span> <span class="s1">&#39;itemID_JGI&#39;</span><span class="p">,</span> <span class="s1">&#39;sampleID_JGI&#39;</span><span class="p">,</span> <span class="s1">&#39;JGI_rawdataname&#39;</span><span class="p">,</span> <span class="s1">&#39;Air_Pressure&#39;</span><span class="p">,</span> <span class="s1">&#39;RH&#39;</span><span class="p">,</span> <span class="s1">&#39;AH&#39;</span><span class="p">,</span> <span class="s1">&#39;Wind_Speed_Mean&#39;</span><span class="p">,</span> <span class="s1">&#39;PAR&#39;</span><span class="p">,</span> 
   <span class="s1">&#39;soil_temp_5_cm_bare_avg&#39;</span><span class="p">,</span> <span class="s1">&#39;soil_temp_5_cm_sod_avg&#39;</span><span class="p">,</span> <span class="s1">&#39;Year&#39;</span><span class="p">,</span> <span class="s1">&#39;date&#39;</span><span class="p">,</span> <span class="s1">&#39;pseudorep&#39;</span><span class="p">,</span><span class="s1">&#39;MMPRNT_ID&#39;</span><span class="p">,</span><span class="s1">&#39;time_zone&#39;</span><span class="p">,</span><span class="s1">&#39;longitude&#39;</span><span class="p">,</span> <span class="s1">&#39;country&#39;</span><span class="p">,</span>
   <span class="s1">&#39;location&#39;</span><span class="p">,</span><span class="s1">&#39;air_temp_max&#39;</span><span class="p">,</span><span class="s1">&#39;Air_Temp_Min&#39;</span><span class="p">,</span><span class="s1">&#39;latitude&#39;</span><span class="p">,</span><span class="s1">&#39;altitude&#39;</span><span class="p">,</span><span class="s1">&#39;plot_name&#39;</span><span class="p">,</span> <span class="s1">&#39;soil_name&#39;</span><span class="p">,</span> <span class="s1">&#39;number_cores&#39;</span><span class="p">,</span> <span class="s1">&#39;Air_temp_mean&#39;</span> <span class="p">,</span>
   <span class="s1">&#39;Wind_Direction_Mean&#39;</span><span class="p">,</span><span class="s1">&#39;time_numeric&#39;</span><span class="p">,</span><span class="s1">&#39;precipitation&#39;</span><span class="p">,</span> <span class="s1">&#39;Solar_Radiation&#39;</span><span class="p">,</span><span class="s1">&#39;pH&#39;</span><span class="p">,</span><span class="s1">&#39;JGI_taxonOID&#39;</span><span class="p">,</span><span class="s1">&#39;JGI_library&#39;</span><span class="p">,</span><span class="s1">&#39;SPNL_date&#39;</span><span class="p">,</span><span class="s1">&#39;lime_index&#39;</span><span class="p">,</span>
   <span class="s1">&#39;P_ppm&#39;</span><span class="p">,</span><span class="s1">&#39;barcode&#39;</span><span class="p">,</span><span class="s1">&#39;K_ppm&#39;</span><span class="p">,</span> <span class="s1">&#39;Ca_ppm&#39;</span><span class="p">,</span> <span class="s1">&#39;Mg_ppm&#39;</span><span class="p">,</span> <span class="s1">&#39;organic_matter&#39;</span><span class="p">,</span> <span class="s1">&#39;NO3N_ppm&#39;</span><span class="p">,</span> <span class="s1">&#39;NH4_ppm&#39;</span><span class="p">,</span> <span class="s1">&#39;soil_moisture_percent&#39;</span><span class="p">,</span> <span class="s1">&#39;soil_temp_10cm&#39;</span><span class="p">,</span> 
   <span class="s1">&#39;plant_name&#39;</span><span class="p">,</span> <span class="s1">&#39;LDMC_mg_per_g&#39;</span><span class="p">,</span> <span class="s1">&#39;nitrogen_percent&#39;</span><span class="p">,</span> <span class="s1">&#39;carbon_percent&#39;</span><span class="p">,</span> <span class="s1">&#39;carbon_per_nitrogen&#39;</span><span class="p">,</span> <span class="s1">&#39;height_mean_cm&#39;</span><span class="p">,</span> <span class="s1">&#39;mass_per_leaf_g&#39;</span><span class="p">,</span>
   <span class="s1">&#39;name&#39;</span><span class="p">,</span><span class="s1">&#39;plotID&#39;</span><span class="p">,</span><span class="s1">&#39;sequence_name&#39;</span><span class="p">],</span><span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span><span class="n">inplace</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="n">metadata</span> <span class="o">=</span> <span class="n">metadata</span><span class="o">.</span><span class="n">rename</span><span class="p">(</span><span class="n">index</span><span class="o">=</span><span class="nb">str</span><span class="p">,</span> <span class="n">columns</span><span class="o">=</span><span class="p">{</span><span class="s1">&#39;nucleic_acid_name&#39;</span><span class="p">:</span><span class="s1">&#39;name&#39;</span><span class="p">})</span>

<span class="c1">#Map Metadata to fastq files</span>
<span class="n">metadata</span><span class="p">[</span><span class="s1">&#39;HPCC_path&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">metadata</span><span class="o">.</span><span class="n">apply</span><span class="p">(</span><span class="k">lambda</span> <span class="n">row</span><span class="p">:</span> <span class="n">lookupFSTQ</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="s1">&#39;name&#39;</span><span class="p">],</span><span class="n">rawFastqFiles</span><span class="p">),</span> <span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>

<span class="c1">#Sort the metadata for ordering purposes</span>
<span class="n">metadata</span><span class="o">.</span><span class="n">sort_values</span><span class="p">(</span><span class="n">by</span><span class="o">=</span><span class="p">[</span><span class="s1">&#39;plant&#39;</span><span class="p">,</span><span class="s1">&#39;sampling_date&#39;</span><span class="p">,</span><span class="s1">&#39;treatment&#39;</span><span class="p">,</span><span class="s1">&#39;name&#39;</span><span class="p">],</span><span class="n">inplace</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span> <span class="c1">#,&quot;Date&quot;,&quot;treatment&quot;,&quot;plot_name&quot;])</span>

<span class="c1">#Change the Identifier</span>
<span class="n">metadata</span><span class="o">.</span><span class="n">set_index</span><span class="p">(</span><span class="s1">&#39;name&#39;</span><span class="p">,</span><span class="n">inplace</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>

<span class="c1">#Show me the top 10</span>
<span class="nb">print</span><span class="p">(</span><span class="n">metadata</span><span class="o">.</span><span class="n">shape</span><span class="p">)</span>
<span class="n">metadata</span><span class="o">.</span><span class="n">head</span><span class="p">(</span><span class="mi">10</span><span class="p">)</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="kn">from</span> <span class="nn">os</span> <span class="k">import</span> <span class="n">listdir</span>
<span class="n">rawDirs</span> <span class="o">=</span> <span class="n">listdir</span><span class="p">(</span><span class="s2">&quot;jgi_transfer/metaT_raw/&quot;</span><span class="p">)</span> <span class="c1">#*/Raw_Data/*</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="kn">from</span> <span class="nn">os</span> <span class="k">import</span> <span class="n">system</span>
<span class="c1"># links = glob(&quot;mapping/metaT/unpaired/*.fastq.gz&quot;)</span>
<span class="c1"># for lnk in links: system(&quot;unlink &quot;+lnk)</span>
<span class="kn">from</span> <span class="nn">os</span> <span class="k">import</span> <span class="n">listdir</span>
<span class="n">rawDirs</span> <span class="o">=</span> <span class="n">listdir</span><span class="p">(</span><span class="s2">&quot;jgi_transfer/metaT_raw/&quot;</span><span class="p">)</span> <span class="c1">#*/Raw_Data/*</span>
<span class="c1">#Make Sym links to put fastqs in same dir</span>
<span class="kn">from</span> <span class="nn">os</span> <span class="k">import</span> <span class="n">system</span>
<span class="k">for</span> <span class="n">sample_name</span> <span class="ow">in</span> <span class="n">metadata</span><span class="o">.</span><span class="n">index</span><span class="p">:</span>
    <span class="k">if</span> <span class="n">metadata</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="n">sample_name</span><span class="p">,</span><span class="s1">&#39;HPCC_path&#39;</span><span class="p">]:</span>
        <span class="k">pass</span>
<span class="c1">#         system(&quot;ln -s /mnt/research/ShadeLab/GLBRC/%s mapping/metaT/unpaired/%s.fastq.gz&quot; % (metadata.loc[sample_name,&#39;HPCC_path&#39;],sample_name))</span>
    <span class="k">else</span><span class="p">:</span> 
        <span class="n">sample_name</span> <span class="o">=</span> <span class="n">sample_name</span><span class="p">[:</span><span class="n">sample_name</span><span class="o">.</span><span class="n">rfind</span><span class="p">(</span><span class="s2">&quot;_&quot;</span><span class="p">)]</span>
        
<span class="c1">#         for fname in rawDirs:</span>
        <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;Missing metadata for&quot;</span><span class="p">,</span><span class="n">sample_name</span><span class="p">)</span>
<span class="c1"># for fname in rawFastqFiles: print(&quot;Missing Metadata:&quot;,fname[fname.find(&quot;function__&quot;)+10:fname.find(&quot;_MT_&quot;)])</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span>%%bash
ls jgi_transfer/metaT_raw/ <span class="p">|</span>wc -l
<span class="nb">cd</span> jgi_transfer/metaT_raw/*G5R4_NF_12JUL2016*
<span class="nb">pwd</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span>%%bash
ls mapping/metaT/unpaired/ <span class="p">|</span>wc -l
ls mapping/metaT/unpaired/*12JUL2016*
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span> 
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="c1"># N-Dimensional Scaling</span>
<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
<span class="kn">from</span> <span class="nn">matplotlib</span> <span class="k">import</span> <span class="n">pyplot</span> <span class="k">as</span> <span class="n">plt</span>
<span class="kn">from</span> <span class="nn">matplotlib.collections</span> <span class="k">import</span> <span class="n">LineCollection</span>
<span class="kn">from</span> <span class="nn">sklearn</span> <span class="k">import</span> <span class="n">manifold</span>
<span class="kn">from</span> <span class="nn">sklearn.metrics</span> <span class="k">import</span> <span class="n">euclidean_distances</span>
<span class="kn">from</span> <span class="nn">sklearn.decomposition</span> <span class="k">import</span> <span class="n">PCA</span>
<span class="kn">from</span> <span class="nn">scipy.spatial</span> <span class="k">import</span> <span class="n">distance</span>

<span class="n">n_samples</span> <span class="o">=</span> <span class="mi">20</span>
<span class="n">seed</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">RandomState</span><span class="p">(</span><span class="n">seed</span><span class="o">=</span><span class="mi">3</span><span class="p">)</span>
<span class="n">X_true</span> <span class="o">=</span> <span class="n">seed</span><span class="o">.</span><span class="n">randint</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">20</span><span class="p">,</span> <span class="mi">2</span> <span class="o">*</span> <span class="n">n_samples</span><span class="p">)</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">float</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="n">X_true</span><span class="p">)</span>
<span class="n">X_true</span> <span class="o">=</span> <span class="n">X_true</span><span class="o">.</span><span class="n">reshape</span><span class="p">((</span><span class="n">n_samples</span><span class="p">,</span> <span class="mi">2</span><span class="p">))</span>

<span class="c1"># Center the data</span>
<span class="c1"># X_true -= X_true.mean()</span>

<span class="n">similarities</span> <span class="o">=</span> <span class="n">euclidean_distances</span><span class="p">(</span><span class="n">X_true</span><span class="p">)</span>
<span class="c1">#print(similarities)</span>

<span class="c1"># Add noise to the similarities</span>
<span class="n">noise</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">rand</span><span class="p">(</span><span class="n">n_samples</span><span class="p">,</span> <span class="n">n_samples</span><span class="p">)</span>
<span class="n">noise</span> <span class="o">=</span> <span class="n">noise</span> <span class="o">+</span> <span class="n">noise</span><span class="o">.</span><span class="n">T</span>
<span class="n">noise</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="n">noise</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">]),</span> <span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="n">noise</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">])]</span> <span class="o">=</span> <span class="mi">0</span>
<span class="c1"># similarities += noise</span>

<span class="n">mds</span> <span class="o">=</span> <span class="n">manifold</span><span class="o">.</span><span class="n">MDS</span><span class="p">(</span><span class="n">n_components</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span> <span class="n">max_iter</span><span class="o">=</span><span class="mi">3000</span><span class="p">,</span> <span class="n">eps</span><span class="o">=</span><span class="mf">1e-9</span><span class="p">,</span> <span class="n">random_state</span><span class="o">=</span><span class="n">seed</span><span class="p">,</span> <span class="n">dissimilarity</span><span class="o">=</span><span class="s2">&quot;precomputed&quot;</span><span class="p">,</span> <span class="n">n_jobs</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
<span class="n">pos</span> <span class="o">=</span> <span class="n">mds</span><span class="o">.</span><span class="n">fit</span><span class="p">(</span><span class="n">similarities</span><span class="p">)</span><span class="o">.</span><span class="n">embedding_</span>

<span class="n">nmds</span> <span class="o">=</span> <span class="n">manifold</span><span class="o">.</span><span class="n">MDS</span><span class="p">(</span><span class="n">n_components</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span> <span class="n">metric</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">max_iter</span><span class="o">=</span><span class="mi">3000</span><span class="p">,</span> <span class="n">eps</span><span class="o">=</span><span class="mf">1e-12</span><span class="p">,</span> <span class="n">dissimilarity</span><span class="o">=</span><span class="s2">&quot;precomputed&quot;</span><span class="p">,</span> <span class="n">random_state</span><span class="o">=</span><span class="n">seed</span><span class="p">,</span> <span class="n">n_jobs</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">n_init</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
<span class="n">npos</span> <span class="o">=</span> <span class="n">nmds</span><span class="o">.</span><span class="n">fit_transform</span><span class="p">(</span><span class="n">similarities</span><span class="p">,</span> <span class="n">init</span><span class="o">=</span><span class="n">pos</span><span class="p">)</span>

<span class="c1"># Rescale the data</span>
<span class="c1"># pos *= np.sqrt((X_true ** 2).sum()) / np.sqrt((pos ** 2).sum())</span>
<span class="c1"># npos *= np.sqrt((X_true ** 2).sum()) / np.sqrt((npos ** 2).sum())</span>

<span class="c1"># Rotate the data</span>
<span class="n">clf</span> <span class="o">=</span> <span class="n">PCA</span><span class="p">(</span><span class="n">n_components</span><span class="o">=</span><span class="mi">2</span><span class="p">)</span>
<span class="n">X_true</span> <span class="o">=</span> <span class="n">clf</span><span class="o">.</span><span class="n">fit_transform</span><span class="p">(</span><span class="n">X_true</span><span class="p">)</span>

<span class="n">pos</span> <span class="o">=</span> <span class="n">clf</span><span class="o">.</span><span class="n">fit_transform</span><span class="p">(</span><span class="n">pos</span><span class="p">)</span>
<span class="n">npos</span> <span class="o">=</span> <span class="n">clf</span><span class="o">.</span><span class="n">fit_transform</span><span class="p">(</span><span class="n">npos</span><span class="p">)</span>

<span class="n">fig</span> <span class="o">=</span> <span class="n">plt</span><span class="o">.</span><span class="n">figure</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span>
<span class="n">ax</span> <span class="o">=</span> <span class="n">plt</span><span class="o">.</span><span class="n">axes</span><span class="p">([</span><span class="mf">0.</span><span class="p">,</span> <span class="mf">0.</span><span class="p">,</span> <span class="mf">1.</span><span class="p">,</span> <span class="mf">1.</span><span class="p">])</span>

<span class="n">s</span> <span class="o">=</span> <span class="mi">100</span>
<span class="n">plt</span><span class="o">.</span><span class="n">scatter</span><span class="p">(</span><span class="n">X_true</span><span class="p">[:,</span> <span class="mi">0</span><span class="p">],</span> <span class="n">X_true</span><span class="p">[:,</span> <span class="mi">1</span><span class="p">],</span> <span class="n">color</span><span class="o">=</span><span class="s1">&#39;navy&#39;</span><span class="p">,</span> <span class="n">s</span><span class="o">=</span><span class="n">s</span><span class="p">,</span> <span class="n">lw</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">label</span><span class="o">=</span><span class="s1">&#39;True Position&#39;</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">scatter</span><span class="p">(</span><span class="n">pos</span><span class="p">[:,</span> <span class="mi">0</span><span class="p">],</span> <span class="n">pos</span><span class="p">[:,</span> <span class="mi">1</span><span class="p">],</span> <span class="n">color</span><span class="o">=</span><span class="s1">&#39;turquoise&#39;</span><span class="p">,</span> <span class="n">s</span><span class="o">=</span><span class="n">s</span><span class="p">,</span> <span class="n">lw</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">label</span><span class="o">=</span><span class="s1">&#39;MDS&#39;</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">scatter</span><span class="p">(</span><span class="n">npos</span><span class="p">[:,</span> <span class="mi">0</span><span class="p">],</span> <span class="n">npos</span><span class="p">[:,</span> <span class="mi">1</span><span class="p">],</span> <span class="n">color</span><span class="o">=</span><span class="s1">&#39;darkorange&#39;</span><span class="p">,</span> <span class="n">s</span><span class="o">=</span><span class="n">s</span><span class="p">,</span> <span class="n">lw</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">label</span><span class="o">=</span><span class="s1">&#39;NMDS&#39;</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">legend</span><span class="p">(</span><span class="n">scatterpoints</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">loc</span><span class="o">=</span><span class="s1">&#39;best&#39;</span><span class="p">,</span> <span class="n">shadow</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
<span class="n">similarities</span> <span class="o">=</span> <span class="n">similarities</span><span class="o">.</span><span class="n">max</span><span class="p">()</span> <span class="o">/</span> <span class="n">similarities</span> <span class="o">*</span> <span class="mi">100</span>
<span class="n">similarities</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">isinf</span><span class="p">(</span><span class="n">similarities</span><span class="p">)]</span> <span class="o">=</span> <span class="mi">0</span>

<span class="c1"># Plot the edges</span>
<span class="n">start_idx</span><span class="p">,</span> <span class="n">end_idx</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">where</span><span class="p">(</span><span class="n">pos</span><span class="p">)</span>
<span class="c1"># a sequence of (*line0*, *line1*, *line2*), where::</span>
<span class="c1">#            linen = (x0, y0), (x1, y1), ... (xm, ym)</span>
<span class="n">segments</span> <span class="o">=</span> <span class="p">[[</span><span class="n">X_true</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="p">:],</span> <span class="n">X_true</span><span class="p">[</span><span class="n">j</span><span class="p">,</span> <span class="p">:]]</span>
            <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">pos</span><span class="p">))</span> <span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">pos</span><span class="p">))]</span>
<span class="n">values</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">abs</span><span class="p">(</span><span class="n">similarities</span><span class="p">)</span>
<span class="n">lc</span> <span class="o">=</span> <span class="n">LineCollection</span><span class="p">(</span><span class="n">segments</span><span class="p">,</span> <span class="n">zorder</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">cmap</span><span class="o">=</span><span class="n">plt</span><span class="o">.</span><span class="n">cm</span><span class="o">.</span><span class="n">Blues</span><span class="p">,</span> <span class="n">norm</span><span class="o">=</span><span class="n">plt</span><span class="o">.</span><span class="n">Normalize</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">values</span><span class="o">.</span><span class="n">max</span><span class="p">()))</span>
<span class="n">lc</span><span class="o">.</span><span class="n">set_array</span><span class="p">(</span><span class="n">similarities</span><span class="o">.</span><span class="n">flatten</span><span class="p">())</span>
<span class="n">lc</span><span class="o">.</span><span class="n">set_linewidths</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">full</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">segments</span><span class="p">),</span> <span class="mf">0.5</span><span class="p">))</span>
<span class="n">ax</span><span class="o">.</span><span class="n">add_collection</span><span class="p">(</span><span class="n">lc</span><span class="p">)</span>

<span class="n">plt</span><span class="o">.</span><span class="n">show</span><span class="p">()</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="kn">from</span> <span class="nn">Bio.SeqIO</span> <span class="k">import</span> <span class="n">parse</span>
<span class="n">dist</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">rec</span> <span class="ow">in</span> <span class="n">parse</span><span class="p">(</span><span class="s2">&quot;assemblies/final.contigs.fa&quot;</span><span class="p">,</span><span class="s2">&quot;fasta&quot;</span><span class="p">):</span> <span class="n">dist</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">rec</span><span class="o">.</span><span class="n">seq</span><span class="p">))</span>
<span class="n">dist</span> <span class="o">=</span> <span class="n">Series</span><span class="p">(</span><span class="n">dist</span><span class="p">)</span>
<span class="n">dist</span><span class="o">.</span><span class="n">plot</span><span class="o">.</span><span class="n">hist</span><span class="p">();</span>
<span class="nb">print</span><span class="p">(</span><span class="n">dist</span><span class="o">.</span><span class="n">describe</span><span class="p">())</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">dist</span><span class="o">.</span><span class="n">plot</span><span class="o">.</span><span class="n">bar</span><span class="p">();</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="kn">from</span> <span class="nn">GetOrfs</span> <span class="k">import</span> <span class="n">getOrfs</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">counter</span> <span class="o">=</span> <span class="mi">0</span>
<span class="n">nfiles</span> <span class="o">=</span> <span class="mi">1</span>
<span class="n">fname</span> <span class="o">=</span> <span class="s2">&quot;contigs2/</span><span class="si">%i</span><span class="s2">.fasta&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">counter</span><span class="p">)</span>
<span class="n">fh</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="s2">&quot;contigs2/</span><span class="si">%i</span><span class="s2">.fasta&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">counter</span><span class="p">),</span><span class="s2">&quot;w&quot;</span><span class="p">)</span>
<span class="k">for</span> <span class="n">rec</span> <span class="ow">in</span> <span class="n">parse</span><span class="p">(</span><span class="s2">&quot;/mnt/scratch/howead/glbrc/assembly/final.contigs.fa&quot;</span><span class="p">,</span><span class="s2">&quot;fasta&quot;</span><span class="p">):</span> 
    <span class="n">write</span><span class="p">(</span><span class="n">rec</span><span class="p">,</span><span class="n">fh</span><span class="p">,</span><span class="s2">&quot;fasta&quot;</span><span class="p">)</span>
    <span class="n">counter</span><span class="o">+=</span><span class="mi">1</span>
    <span class="k">if</span> <span class="p">(</span><span class="n">counter</span> <span class="o">%</span> <span class="mi">5000</span> <span class="o">==</span> <span class="mi">0</span><span class="p">):</span>
        <span class="n">fh</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
        <span class="n">getOrfs</span><span class="p">(</span><span class="n">fname</span><span class="p">)</span>
        <span class="n">nfiles</span><span class="o">+=</span><span class="mi">1</span>
        <span class="n">fname</span> <span class="o">=</span> <span class="s2">&quot;contigs2/</span><span class="si">%i</span><span class="s2">.fasta&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">counter</span><span class="p">)</span>
        <span class="n">fh</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="s2">&quot;contigs2/</span><span class="si">%i</span><span class="s2">.fasta&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">counter</span><span class="p">),</span><span class="s2">&quot;w&quot;</span><span class="p">)</span>
<span class="n">fh</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
<span class="c1">#pickle.dump(contigNames,open(&quot;SeqIDs.p&quot;, &quot;wb&quot;))</span>
<span class="c1">#contigNames = pickle.load(open(&quot;SeqIDs.p&quot;, &quot;rb&quot;))</span>
<span class="c1">#files = glob(&quot;bams/*.bam&quot;)</span>
<span class="nb">print</span><span class="p">(</span><span class="n">nfiles</span><span class="p">)</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span>%%bash
ls -alh pickles/G5R3_NF_31MAY2016_LD1_counts.p
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="kn">import</span> <span class="nn">pickle</span>
<span class="n">files</span> <span class="o">=</span> <span class="n">glob</span><span class="p">(</span><span class="s2">&quot;stats/*.tsv&quot;</span><span class="p">)</span>
<span class="nb">print</span> <span class="p">(</span><span class="s2">&quot;Number of files:&quot;</span><span class="p">,</span><span class="nb">len</span><span class="p">(</span><span class="n">files</span><span class="p">))</span>
<span class="n">smallFile</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="s2">&quot;testFile.txt&quot;</span><span class="p">,</span><span class="s2">&quot;w&quot;</span><span class="p">)</span>

<span class="k">for</span> <span class="n">statFile</span> <span class="ow">in</span> <span class="n">files</span><span class="p">:</span>
    <span class="n">counter</span> <span class="o">=</span> <span class="mi">0</span>
    <span class="n">readsFileName</span> <span class="o">=</span> <span class="n">statFile</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;stats/&quot;</span><span class="p">,</span><span class="s2">&quot;&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;.tsv&quot;</span><span class="p">,</span><span class="s2">&quot;&quot;</span><span class="p">)</span>
    <span class="n">sampleMeta</span> <span class="o">=</span> <span class="n">metadata</span><span class="p">[</span><span class="n">metadata</span><span class="o">.</span><span class="n">index</span> <span class="o">==</span> <span class="n">readsFileName</span><span class="p">]</span>
    <span class="n">curSampleID</span> <span class="o">=</span> <span class="n">sampleMeta</span><span class="o">.</span><span class="n">nucleic_acid_name</span><span class="o">.</span><span class="n">values</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>

    <span class="n">fname</span> <span class="o">=</span> <span class="s2">&quot;pickles/</span><span class="si">%s</span><span class="s2">_counts.p&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">curSampleID</span><span class="p">)</span>
    <span class="n">fh</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">fname</span><span class="p">,</span><span class="s2">&quot;rb&quot;</span><span class="p">)</span>
    <span class="n">data</span> <span class="o">=</span> <span class="n">pickle</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">fh</span><span class="p">)</span>
    <span class="nb">print</span><span class="p">(</span><span class="n">data</span><span class="p">)</span>
    <span class="k">break</span>

<span class="n">smallFile</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="kn">from</span> <span class="nn">glob</span> <span class="k">import</span> <span class="n">glob</span>
<span class="kn">from</span> <span class="nn">os</span> <span class="k">import</span> <span class="n">path</span>
<span class="n">sample_data</span> <span class="o">=</span> <span class="p">{}</span>
<span class="n">files</span> <span class="o">=</span> <span class="n">glob</span><span class="p">(</span><span class="s2">&quot;stats/*.tsv&quot;</span><span class="p">)</span>
<span class="nb">print</span> <span class="p">(</span><span class="s2">&quot;Number of files:&quot;</span><span class="p">,</span><span class="nb">len</span><span class="p">(</span><span class="n">files</span><span class="p">))</span>
<span class="n">counter</span> <span class="o">=</span> <span class="mi">0</span>
<span class="k">for</span> <span class="n">statFile</span> <span class="ow">in</span> <span class="n">files</span><span class="p">:</span>
    <span class="n">readsFileName</span> <span class="o">=</span> <span class="n">statFile</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;stats/&quot;</span><span class="p">,</span><span class="s2">&quot;&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;.tsv&quot;</span><span class="p">,</span><span class="s2">&quot;&quot;</span><span class="p">)</span>
    <span class="n">sampleMeta</span> <span class="o">=</span> <span class="n">metadata</span><span class="p">[</span><span class="n">metadata</span><span class="o">.</span><span class="n">index</span> <span class="o">==</span> <span class="n">readsFileName</span><span class="p">]</span>
    <span class="n">curSampleID</span> <span class="o">=</span> <span class="n">sampleMeta</span><span class="o">.</span><span class="n">nucleic_acid_name</span><span class="o">.</span><span class="n">values</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
    <span class="n">sample_data</span><span class="o">=</span><span class="p">{}</span>
    <span class="n">counter</span><span class="o">+=</span><span class="mi">1</span>
    <span class="nb">print</span> <span class="p">(</span><span class="s2">&quot;</span><span class="si">%i</span><span class="s2">. </span><span class="si">%s</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">counter</span><span class="p">,</span> <span class="n">curSampleID</span><span class="p">))</span>
<span class="c1">#     if path.exists(&quot;pickles/%s_counts.p&quot; % (curSampleID)):continue#</span>
<span class="c1">#     for line in open(statFile):</span>
<span class="c1">#         rec = line.strip().split()</span>
<span class="c1">#         sample_data[rec[0]] = int(rec[2]) #How can an unmapped read be connected to a contig?</span>
<span class="c1">#     pickle.dump(sample_data,open(&quot;pickles/%s_counts.p&quot; % (curSampleID),&quot;wb&quot;))</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="c1">#Dimensional Reduction</span>
<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>

<span class="kn">from</span> <span class="nn">matplotlib</span> <span class="k">import</span> <span class="n">pyplot</span> <span class="k">as</span> <span class="n">plt</span>
<span class="kn">from</span> <span class="nn">matplotlib.collections</span> <span class="k">import</span> <span class="n">LineCollection</span>
<span class="kn">from</span> <span class="nn">sklearn</span> <span class="k">import</span> <span class="n">manifold</span>
<span class="kn">from</span> <span class="nn">sklearn.metrics</span> <span class="k">import</span> <span class="n">euclidean_distances</span>
<span class="kn">from</span> <span class="nn">sklearn.decomposition</span> <span class="k">import</span> <span class="n">PCA</span>
</pre></div>

    </div>
</div>
</div>

  </div>
<div class="cell border-box-sizing text_cell rendered"><div class="inner_cell">
<div class="text_cell_render border-box-sizing rendered_html">

</div>
</div>
</div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="k">def</span> <span class="nf">checkSkipRead</span><span class="p">(</span><span class="n">read</span><span class="p">,</span><span class="n">reads</span><span class="p">):</span>
    <span class="c1"># 1. Read is unmapped</span>
    <span class="c1"># 2. Read pair has already been seen </span>
    <span class="c1"># 3. Read doesn&#39;t map well</span>
    <span class="k">return</span> <span class="n">read</span><span class="o">.</span><span class="n">is_unmapped</span> <span class="ow">or</span> <span class="n">read</span><span class="o">.</span><span class="n">qname</span> <span class="ow">in</span> <span class="n">reads</span> <span class="ow">or</span> <span class="n">read</span><span class="o">.</span><span class="n">mapping_quality</span> <span class="o">&lt;=</span> <span class="mi">20</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">count</span> <span class="o">=</span> <span class="mi">0</span>

<span class="k">for</span> <span class="n">bamFileName</span> <span class="ow">in</span> <span class="n">files</span><span class="p">:</span>
    <span class="n">contigCounter</span> <span class="o">=</span> <span class="n">contigNames</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
    <span class="n">samfile</span> <span class="o">=</span> <span class="n">pysam</span><span class="o">.</span><span class="n">AlignmentFile</span><span class="p">(</span><span class="n">bamFileName</span><span class="p">,</span> <span class="s2">&quot;rb&quot;</span><span class="p">)</span>
    <span class="n">readsFileName</span> <span class="o">=</span> <span class="n">bamFileName</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;bams/&quot;</span><span class="p">,</span><span class="s2">&quot;&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;.sorted.bam&quot;</span><span class="p">,</span><span class="s2">&quot;&quot;</span><span class="p">)</span>
    <span class="nb">print</span> <span class="n">readsFileName</span>
    <span class="n">sampleMeta</span> <span class="o">=</span> <span class="n">metadata</span><span class="p">[</span><span class="n">metadata</span><span class="o">.</span><span class="n">index</span> <span class="o">==</span> <span class="n">readsFileName</span><span class="p">]</span>
    <span class="n">nuceID</span> <span class="o">=</span> <span class="n">sampleMeta</span><span class="o">.</span><span class="n">nucleic_acid_name</span><span class="o">.</span><span class="n">get_values</span><span class="p">()[</span><span class="mi">0</span><span class="p">]</span>
    <span class="n">countsFile</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="s2">&quot;counts/</span><span class="si">%s</span><span class="s2">.txt&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">nuceID</span><span class="p">),</span><span class="s2">&quot;w&quot;</span><span class="p">)</span>
    <span class="n">reads</span><span class="o">=</span><span class="nb">set</span><span class="p">()</span>
    <span class="k">for</span> <span class="n">read</span> <span class="ow">in</span> <span class="n">samfile</span><span class="p">:</span>
        <span class="k">if</span> <span class="n">checkSkipRead</span><span class="p">(</span><span class="n">read</span><span class="p">,</span><span class="n">reads</span><span class="p">):</span><span class="k">continue</span> 
        <span class="n">reads</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">read</span><span class="o">.</span><span class="n">qname</span><span class="p">)</span>
    <span class="n">countsFile</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
    <span class="k">break</span>
<span class="nb">print</span> <span class="n">coninues</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="nb">print</span> <span class="n">samFileName</span>
<span class="n">counter</span> <span class="o">=</span> <span class="mi">0</span>
<span class="k">for</span> <span class="n">name</span> <span class="ow">in</span> <span class="n">contigCounter</span><span class="p">:</span>
    <span class="nb">print</span> <span class="n">name</span><span class="p">,</span> <span class="n">samfile</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="n">name</span><span class="p">)</span>
    <span class="n">counter</span> <span class="o">+=</span><span class="mi">1</span>
    <span class="k">if</span> <span class="n">counter</span> <span class="o">==</span> <span class="mi">10</span><span class="p">:</span> <span class="k">break</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="nb">print</span> <span class="s2">&quot;Number of unmapped&quot;</span><span class="p">,</span><span class="n">unmapped</span>
<span class="nb">print</span> <span class="n">coninues</span><span class="o">-</span><span class="n">unmapped</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="nb">print</span> <span class="n">read</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="nb">print</span> <span class="n">read</span><span class="o">.</span><span class="n">reference_name</span>
<span class="nb">print</span> <span class="n">samFileName</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">contname</span> <span class="o">=</span> <span class="n">contigNames</span><span class="o">.</span><span class="n">keys</span><span class="p">()[</span><span class="mi">0</span><span class="p">]</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">files</span> <span class="o">=</span> <span class="n">glob</span><span class="p">(</span><span class="s2">&quot;stats/*.tsv&quot;</span><span class="p">)</span>
<span class="n">sampleStats</span> <span class="o">=</span> <span class="p">{}</span>
<span class="k">for</span> <span class="n">statFile</span> <span class="ow">in</span> <span class="n">files</span><span class="p">:</span>
    <span class="n">sampleFileName</span> <span class="o">=</span> <span class="n">statFile</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;stats/&quot;</span><span class="p">,</span><span class="s2">&quot;&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;.tsv&quot;</span><span class="p">,</span><span class="s2">&quot;&quot;</span><span class="p">)</span>
    <span class="n">sampleMeta</span> <span class="o">=</span> <span class="n">metadata</span><span class="p">[</span><span class="n">metadata</span><span class="o">.</span><span class="n">index</span> <span class="o">==</span> <span class="n">sampleFileName</span><span class="p">]</span>
    <span class="n">nuceID</span> <span class="o">=</span> <span class="n">sampleMeta</span><span class="o">.</span><span class="n">nucleic_acid_name</span><span class="o">.</span><span class="n">get_values</span><span class="p">()[</span><span class="mi">0</span><span class="p">]</span>
    <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">open</span><span class="p">(</span><span class="n">statFile</span><span class="p">):</span>
        <span class="n">rec</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">()</span>
        <span class="n">contigNames</span><span class="p">[</span><span class="n">rec</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">rec</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>
    <span class="n">sampleStats</span><span class="p">[</span><span class="n">nuceID</span><span class="p">]</span> <span class="o">=</span> <span class="n">contigNames</span>
<span class="kn">import</span> <span class="nn">pickle</span>
<span class="n">pickle</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="n">sampleStats</span><span class="p">,</span><span class="nb">open</span><span class="p">(</span><span class="s2">&quot;sampleCounts.p&quot;</span><span class="p">,</span><span class="s2">&quot;wb&quot;</span><span class="p">))</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">help</span><span class="p">(</span><span class="n">samfile</span><span class="o">.</span><span class="n">count</span><span class="p">)</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">counter</span> <span class="o">=</span> <span class="mi">0</span>
<span class="k">for</span> <span class="nb">id</span> <span class="ow">in</span> <span class="n">metadata</span><span class="o">.</span><span class="n">index</span><span class="p">:</span>
    <span class="k">if</span> <span class="s1">&#39;11505.2.209522.CACCTTA-GTAAGGT.fastq.gz&#39;</span> <span class="ow">in</span> <span class="nb">id</span><span class="p">:</span> 
        <span class="n">counter</span> <span class="o">+=</span> <span class="mi">1</span>
        <span class="nb">print</span> <span class="nb">id</span><span class="p">,</span>
        <span class="k">if</span> <span class="n">counter</span> <span class="o">%</span> <span class="mi">2</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span><span class="nb">print</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">sampleMeta</span> <span class="o">=</span> <span class="n">metadata</span><span class="p">[</span><span class="n">metadata</span><span class="o">.</span><span class="n">index</span> <span class="o">==</span> <span class="n">readsFileName</span><span class="p">]</span>
<span class="n">sampleMeta</span><span class="o">.</span><span class="n">nucleic_acid_name</span><span class="o">.</span><span class="n">get_values</span><span class="p">()[</span><span class="mi">0</span><span class="p">]</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">samFileName</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">rec</span><span class="o">.</span><span class="n">is_qcfail</span>
<span class="n">rec</span><span class="o">.</span><span class="n">is_read1</span>
<span class="nb">dir</span><span class="p">(</span><span class="n">rec</span><span class="p">)</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="nb">print</span> <span class="mi">10</span><span class="o">**</span><span class="p">(</span><span class="o">-</span><span class="p">(</span><span class="nb">ord</span><span class="p">(</span><span class="s1">&#39;3&#39;</span><span class="p">)</span><span class="o">-</span><span class="mi">33</span><span class="p">)</span><span class="o">/</span><span class="mf">10.0</span><span class="p">)</span>
<span class="nb">print</span> <span class="mf">10.0</span><span class="o">**</span><span class="p">(</span><span class="o">-</span><span class="p">(</span><span class="nb">ord</span><span class="p">(</span><span class="s1">&#39;3&#39;</span><span class="p">)</span><span class="o">-</span><span class="mf">33.0</span><span class="p">)</span><span class="o">/</span><span class="mf">10.0</span><span class="p">)</span>
<span class="nb">print</span> <span class="mi">10</span><span class="o">**</span><span class="p">(</span><span class="o">-</span><span class="p">(</span><span class="nb">ord</span><span class="p">(</span><span class="s1">&#39;3&#39;</span><span class="p">)</span><span class="o">-</span><span class="mi">33</span><span class="p">)</span><span class="o">/</span><span class="mi">10</span><span class="p">)</span>
<span class="nb">print</span> <span class="mi">10</span><span class="o">**</span><span class="p">(</span><span class="o">-</span><span class="p">(</span><span class="nb">ord</span><span class="p">(</span><span class="s1">&#39;3&#39;</span><span class="p">)</span><span class="o">-</span><span class="mf">33.0</span><span class="p">)</span><span class="o">/</span><span class="mi">10</span><span class="p">)</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span>%%bash
<span class="nb">pwd</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="kn">from</span> <span class="nn">glob</span> <span class="k">import</span> <span class="n">glob</span>
<span class="n">fh</span><span class="o">=</span><span class="nb">open</span><span class="p">(</span><span class="s2">&quot;CombinedStats.tsv&quot;</span><span class="p">,</span><span class="s2">&quot;w&quot;</span><span class="p">)</span>
<span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">&quot;Contig&quot;</span><span class="p">)</span>

<span class="k">for</span> <span class="n">fname</span> <span class="ow">in</span> <span class="n">glob</span><span class="p">(</span><span class="s2">&quot;stats/*.tsv&quot;</span><span class="p">):</span>
    <span class="nb">print</span><span class="p">(</span><span class="n">fname</span><span class="p">)</span>
    <span class="n">readsFileName</span> <span class="o">=</span> <span class="n">fname</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;stats/&quot;</span><span class="p">,</span><span class="s2">&quot;&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;.tsv&quot;</span><span class="p">,</span><span class="s2">&quot;&quot;</span><span class="p">)</span>
    <span class="n">sampleMeta</span> <span class="o">=</span> <span class="n">metadata</span><span class="p">[</span><span class="n">metadata</span><span class="o">.</span><span class="n">index</span> <span class="o">==</span> <span class="n">readsFileName</span><span class="p">]</span>
    <span class="n">curSampleID</span> <span class="o">=</span> <span class="n">sampleMeta</span><span class="o">.</span><span class="n">nucleic_acid_name</span><span class="o">.</span><span class="n">values</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
    <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="o">+</span><span class="n">curSampleID</span><span class="p">)</span>


<span class="c1">#Get the column identifier</span>
<span class="n">init_fname</span> <span class="o">=</span> <span class="s2">&quot;stats/11425.3.206650.ACGGTCT-AAGACCG.fastq.gz.tsv&quot;</span>
<span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">open</span><span class="p">(</span><span class="n">init_fname</span><span class="p">):</span>
    <span class="n">rec</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">()</span>
    <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="o">+</span><span class="n">rec</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
<span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">&quot;</span><span class="se">\n</span><span class="s2">&quot;</span><span class="p">)</span>

<span class="c1">#Read all the files</span>
<span class="k">for</span> <span class="n">fname</span> <span class="ow">in</span> <span class="n">glob</span><span class="p">(</span><span class="s2">&quot;stats/*.tsv&quot;</span><span class="p">):</span>
    <span class="nb">print</span><span class="p">(</span><span class="n">fname</span><span class="p">)</span>
    <span class="n">readsFileName</span> <span class="o">=</span> <span class="n">fname</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;stats/&quot;</span><span class="p">,</span><span class="s2">&quot;&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;.tsv&quot;</span><span class="p">,</span><span class="s2">&quot;&quot;</span><span class="p">)</span>
    <span class="n">sampleMeta</span> <span class="o">=</span> <span class="n">metadata</span><span class="p">[</span><span class="n">metadata</span><span class="o">.</span><span class="n">index</span> <span class="o">==</span> <span class="n">readsFileName</span><span class="p">]</span>
    <span class="n">curSampleID</span> <span class="o">=</span> <span class="n">sampleMeta</span><span class="o">.</span><span class="n">nucleic_acid_name</span><span class="o">.</span><span class="n">values</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
    <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">curSampleID</span><span class="p">)</span>
    <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">open</span><span class="p">(</span><span class="n">fname</span><span class="p">):</span>
        <span class="n">rec</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">()</span>
        <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="o">+</span><span class="n">rec</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>
    <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">&quot;</span><span class="se">\n</span><span class="s2">&quot;</span><span class="p">)</span>
<span class="n">fh</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="kn">import</span> <span class="nn">linecache</span>
<span class="kn">from</span> <span class="nn">glob</span> <span class="k">import</span> <span class="n">glob</span>
<span class="c1"># fh = open(&quot;CombinedStats_T.tsv&quot;,&quot;w&quot;)</span>
<span class="c1"># fh.write(&quot;\t&quot;)</span>
<span class="n">fileNames</span> <span class="o">=</span> <span class="n">glob</span><span class="p">(</span><span class="s2">&quot;stats/*.tsv&quot;</span><span class="p">)</span>

<span class="c1"># #Write the header line</span>
<span class="c1"># for fname in fileNames:</span>
<span class="c1">#     readsFileName = fname.replace(&quot;stats/&quot;,&quot;&quot;).replace(&quot;.tsv&quot;,&quot;&quot;)</span>
<span class="c1">#     sampleMeta = metadata[metadata.index == readsFileName]</span>
<span class="c1">#     curSampleID = sampleMeta.nucleic_acid_name.values[0]</span>
<span class="c1">#     fh.write(&quot;\t&quot;+curSampleID)</span>
<span class="c1"># fh.write(&quot;\n&quot;)</span>

<span class="c1">#get the row starters</span>
<span class="n">pres_abs</span> <span class="o">=</span> <span class="p">{}</span>
<span class="n">total_count</span> <span class="o">=</span>
<span class="n">init_fname</span> <span class="o">=</span> <span class="s2">&quot;stats/11425.3.206650.ACGGTCT-AAGACCG.fastq.gz.tsv&quot;</span>
<span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">open</span><span class="p">(</span><span class="n">init_fname</span><span class="p">):</span> <span class="n">rows</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">()[</span><span class="mi">0</span><span class="p">])</span>
<span class="nb">print</span><span class="p">(</span><span class="s2">&quot;Done getting contig names&quot;</span><span class="p">)</span>
<span class="n">fh</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="s2">&quot;combined/CombinedStats_T</span><span class="si">%i</span><span class="s2">.tsv&quot;</span> <span class="o">%</span> <span class="mi">0</span> <span class="p">,</span><span class="s2">&quot;w&quot;</span><span class="p">)</span>
<span class="n">val</span><span class="o">=</span><span class="p">{</span><span class="mi">0</span><span class="p">:</span><span class="s2">&quot;&quot;</span><span class="p">}</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span><span class="mi">12301484</span><span class="p">):</span>
    <span class="nb">print</span><span class="p">(</span><span class="n">i</span><span class="p">,</span><span class="n">end</span><span class="o">=</span><span class="s2">&quot; &quot;</span><span class="p">)</span>
    <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">rows</span><span class="p">[</span><span class="n">i</span><span class="o">-</span><span class="mi">1</span><span class="p">])</span>
    <span class="k">for</span> <span class="n">fname</span> <span class="ow">in</span> <span class="n">fileNames</span><span class="p">:</span> <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="o">+</span><span class="n">linecache</span><span class="o">.</span><span class="n">getline</span><span class="p">(</span><span class="n">fname</span><span class="p">,</span> <span class="n">i</span><span class="p">))</span>
    <span class="n">fh</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">&quot;</span><span class="se">\n</span><span class="s2">&quot;</span><span class="p">)</span>
    <span class="k">try</span><span class="p">:</span>
        <span class="n">val</span><span class="p">[</span><span class="n">i</span> <span class="o">%</span>  <span class="mi">5000</span><span class="p">]</span> <span class="o">=</span> <span class="mi">1</span>
        <span class="nb">print</span><span class="p">(</span><span class="n">i</span><span class="p">,</span><span class="n">end</span><span class="o">=</span><span class="s2">&quot; &quot;</span><span class="p">)</span>
        <span class="n">fh</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
        <span class="n">fh</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="s2">&quot;combined/CombinedStats_T</span><span class="si">%i</span><span class="s2">.tsv&quot;</span> <span class="o">%</span> <span class="n">i</span> <span class="p">,</span><span class="s2">&quot;w&quot;</span><span class="p">)</span>
    <span class="k">except</span><span class="p">:</span><span class="k">pass</span>
        
<span class="nb">print</span><span class="p">(</span><span class="s2">&quot;Done&quot;</span><span class="p">)</span>    
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="c1"># Presence absence</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="kn">from</span> <span class="nn">glob</span> <span class="k">import</span> <span class="n">glob</span>
<span class="kn">import</span> <span class="nn">pickle</span>
<span class="n">fileNames</span> <span class="o">=</span> <span class="n">glob</span><span class="p">(</span><span class="s2">&quot;stats/*.tsv&quot;</span><span class="p">)</span>
<span class="n">presAbs</span><span class="p">,</span><span class="n">abundance</span> <span class="o">=</span> <span class="p">{},{}</span>

<span class="k">for</span> <span class="n">fname</span> <span class="ow">in</span> <span class="n">fileNames</span><span class="p">:</span>
    <span class="nb">print</span><span class="p">(</span><span class="n">fname</span><span class="p">)</span>
    <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">open</span><span class="p">(</span><span class="n">fname</span><span class="p">):</span> 
        <span class="n">rec</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">()</span>
        <span class="k">try</span><span class="p">:</span><span class="n">presAbs</span><span class="p">[</span><span class="n">rec</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span> <span class="o">+=</span> <span class="nb">int</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">rec</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">)</span>
        <span class="k">except</span><span class="p">:</span><span class="n">presAbs</span><span class="p">[</span><span class="n">rec</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">rec</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">)</span>
        <span class="k">try</span><span class="p">:</span><span class="n">abundance</span><span class="p">[</span><span class="n">rec</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span> <span class="o">+=</span> <span class="nb">int</span><span class="p">(</span><span class="n">rec</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>
        <span class="k">except</span><span class="p">:</span><span class="n">abundance</span><span class="p">[</span><span class="n">rec</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">rec</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>

<span class="n">pickle</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="n">presAbs</span><span class="p">,</span><span class="nb">open</span><span class="p">(</span><span class="s2">&quot;presence_Absence.p&quot;</span><span class="p">,</span><span class="s2">&quot;wb&quot;</span><span class="p">))</span>    
<span class="n">pickle</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="n">abundance</span><span class="p">,</span><span class="nb">open</span><span class="p">(</span><span class="s2">&quot;abundance.p&quot;</span><span class="p">,</span><span class="s2">&quot;wb&quot;</span><span class="p">))</span>   
<span class="nb">print</span><span class="p">(</span><span class="s2">&quot;Done&quot;</span><span class="p">)</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">dist</span><span class="o">.</span><span class="n">describe</span><span class="p">()</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">dist_abu</span> <span class="o">=</span> <span class="p">[]</span>
<span class="nb">print</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">fileNames</span><span class="p">)</span><span class="o">*.</span><span class="mi">7</span><span class="p">),</span><span class="nb">len</span><span class="p">(</span><span class="n">fileNames</span><span class="p">))</span>
<span class="n">numSamples</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">fileNames</span><span class="p">))</span>
<span class="k">for</span> <span class="n">contig</span><span class="p">,</span> <span class="n">count</span> <span class="ow">in</span> <span class="n">abundance</span><span class="o">.</span><span class="n">items</span><span class="p">():</span> <span class="n">dist_abu</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">count</span><span class="o">/</span><span class="n">numSamples</span><span class="p">)</span>
    
<span class="kn">from</span> <span class="nn">pandas</span> <span class="k">import</span> <span class="n">Series</span>
<span class="n">dist</span> <span class="o">=</span> <span class="n">Series</span><span class="p">(</span><span class="n">dist_abu</span><span class="p">)</span>
<span class="n">dist</span><span class="o">.</span><span class="n">plot</span><span class="o">.</span><span class="n">hist</span><span class="p">();</span>
<span class="n">dist</span><span class="o">.</span><span class="n">describe</span><span class="p">()</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">dist</span><span class="o">.</span><span class="n">describe</span><span class="p">()</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="c1">#Combining Sample Counts</span>

<span class="n">allCounts</span> <span class="o">=</span> <span class="n">load</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="s2">&quot;pickles/allCounts_genes.p&quot;</span><span class="p">,</span><span class="s2">&quot;rb&quot;</span><span class="p">))</span> 

<span class="n">combined_abundance</span> <span class="o">=</span> <span class="p">{}</span>
<span class="k">for</span> <span class="n">crop</span> <span class="ow">in</span> <span class="nb">set</span><span class="p">(</span><span class="n">metadata</span><span class="o">.</span><span class="n">type</span><span class="p">):</span>
    <span class="k">for</span> <span class="n">date</span> <span class="ow">in</span> <span class="nb">set</span><span class="p">(</span><span class="n">metadata</span><span class="o">.</span><span class="n">sampling_date</span><span class="p">):</span>
        <span class="k">for</span> <span class="n">treatment</span> <span class="ow">in</span> <span class="nb">set</span><span class="p">(</span><span class="n">metadata</span><span class="o">.</span><span class="n">treatment</span><span class="p">):</span>
            <span class="n">sampleGroupMeta</span> <span class="o">=</span> <span class="n">metadata</span><span class="o">.</span><span class="n">loc</span><span class="p">[(</span><span class="n">metadata</span><span class="o">.</span><span class="n">sampling_date</span><span class="o">==</span><span class="n">date</span><span class="p">)</span> <span class="o">&amp;</span> <span class="p">(</span><span class="n">metadata</span><span class="o">.</span><span class="n">treatment</span><span class="o">==</span><span class="n">treatment</span><span class="p">)</span> <span class="o">&amp;</span> <span class="p">(</span><span class="n">metadata</span><span class="o">.</span><span class="n">type</span> <span class="o">==</span> <span class="n">crop</span><span class="p">)]</span>
            <span class="n">groupName</span> <span class="o">=</span> <span class="s2">&quot;</span><span class="si">%s</span><span class="s2">_</span><span class="si">%s</span><span class="s2">_</span><span class="si">%s</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">crop</span><span class="p">,</span><span class="n">treatment</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot; &quot;</span><span class="p">,</span><span class="s2">&quot;&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">&quot;f&quot;</span><span class="p">,</span><span class="s2">&quot;F&quot;</span><span class="p">),</span><span class="n">date</span><span class="p">)</span>
            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">sampleGroupMeta</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span> <span class="k">continue</span>
            <span class="nb">print</span><span class="p">(</span><span class="n">groupName</span><span class="p">)</span>
            <span class="n">combined_abundance</span><span class="p">[</span><span class="n">groupName</span><span class="p">]</span><span class="o">=</span> <span class="p">{}</span>
            <span class="k">for</span> <span class="n">sampleName</span> <span class="ow">in</span> <span class="n">sampleGroupMeta</span><span class="o">.</span><span class="n">nucleic_acid_name</span><span class="p">:</span>
                <span class="c1">#print(sampleName,len(allCounts[sampleName]))</span>
                <span class="k">for</span> <span class="n">rec</span><span class="p">,</span><span class="n">count</span> <span class="ow">in</span> <span class="n">allCounts</span><span class="p">[</span><span class="n">sampleName</span><span class="p">]</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
                    <span class="k">try</span><span class="p">:</span><span class="n">combined_abundance</span><span class="p">[</span><span class="n">groupName</span><span class="p">][</span><span class="n">rec</span><span class="p">]</span> <span class="o">+=</span> <span class="n">count</span>
                    <span class="k">except</span><span class="p">:</span><span class="n">combined_abundance</span><span class="p">[</span><span class="n">groupName</span><span class="p">][</span><span class="n">rec</span><span class="p">]</span> <span class="o">=</span> <span class="n">count</span>
<span class="n">allCounts</span> <span class="o">=</span> <span class="n">DataFrame</span><span class="p">(</span><span class="n">combined_abundance</span><span class="p">)</span>
<span class="n">allCounts</span><span class="p">[</span><span class="s2">&quot;Average&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="n">allCounts</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span><span class="o">/</span><span class="nb">float</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">metadata</span><span class="o">.</span><span class="n">index</span><span class="p">))</span>
<span class="n">allCounts</span><span class="p">[</span><span class="s2">&quot;Average&quot;</span><span class="p">]</span><span class="o">.</span><span class="n">head</span><span class="p">()</span>
<span class="c1">#allCounts.drop(&quot;Average&quot;,axis=1,inplace=True)</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="k">for</span> <span class="n">fname</span> <span class="ow">in</span> <span class="n">metadata</span><span class="o">.</span><span class="n">index</span><span class="p">:</span>
    <span class="n">sampMet</span> <span class="o">=</span> <span class="n">metadata</span><span class="p">[</span><span class="n">metadata</span><span class="o">.</span><span class="n">index</span> <span class="o">==</span> <span class="n">fname</span><span class="p">]</span>
    <span class="n">sampleID</span> <span class="o">=</span> <span class="n">sampMet</span><span class="o">.</span><span class="n">nucleic_acid_name</span><span class="o">.</span><span class="n">unique</span><span class="p">()[</span><span class="mi">0</span><span class="p">]</span>
    <span class="c1">#print(&quot;mv mapping/flagstats/%s.stat mapping/flagstats/%s.stat&quot; % (fname,sampleID))</span>
    
    <span class="n">res</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">system</span><span class="p">(</span><span class="s2">&quot;mv mapping/flagstats/</span><span class="si">%s</span><span class="s2">.stat mapping/flagstats/</span><span class="si">%s</span><span class="s2">.txt&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">sampleID</span><span class="p">,</span><span class="n">sampleID</span><span class="p">))</span>
    <span class="nb">print</span><span class="p">(</span><span class="n">fname</span><span class="p">,</span><span class="n">res</span><span class="p">)</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">v</span><span class="o">=</span> <span class="n">MultiqcModule</span><span class="p">()</span>
<span class="n">v</span> <span class="o">=</span> <span class="n">FlagstatReportMixin</span><span class="p">()</span>
<span class="n">v</span><span class="o">.</span><span class="n">parse_samtools_flagstats</span><span class="p">()</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="kn">from</span> <span class="nn">__future__</span> <span class="k">import</span> <span class="n">print_function</span>
<span class="kn">from</span> <span class="nn">collections</span> <span class="k">import</span> <span class="n">OrderedDict</span>
<span class="kn">import</span> <span class="nn">logging</span>
<span class="kn">import</span> <span class="nn">re</span>

<span class="kn">from</span> <span class="nn">multiqc</span> <span class="k">import</span> <span class="n">config</span>
<span class="kn">from</span> <span class="nn">multiqc.plots</span> <span class="k">import</span> <span class="n">bargraph</span>
<span class="kn">from</span> <span class="nn">multiqc.modules.base_module</span> <span class="k">import</span> <span class="n">BaseMultiqcModule</span>
<span class="c1"># from multiqc.utils import config as mqcConfig</span>
<span class="c1"># def load_config():</span>
<span class="c1">#     my_search_patterns = {</span>
<span class="c1">#         &#39;my_plugin/my_mod&#39;: {&#39;fn&#39;: &#39;*_somefile.txt&#39;},</span>
<span class="c1">#         &#39;my_plugin/my_other_mod&#39;: {&#39;fn&#39;: &#39;*other_file.txt&#39;},</span>
<span class="c1">#     }</span>
<span class="c1">#     mqcConfig.update_dict(config.sp, my_search_patterns)</span>


<span class="c1"># Initialise the logger</span>
<span class="n">log</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="vm">__name__</span><span class="p">)</span>

<span class="k">class</span> <span class="nc">MultiqcModule</span><span class="p">(</span><span class="n">BaseMultiqcModule</span><span class="p">):</span>
    <span class="sd">&quot;&quot;&quot; Bowtie 2 module, parses stderr logs. &quot;&quot;&quot;</span>

    <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>

        <span class="c1"># Initialise the parent object</span>
        <span class="nb">super</span><span class="p">(</span><span class="n">MultiqcModule</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s2">&quot;Bowtie 2&quot;</span><span class="p">,</span> <span class="n">anchor</span><span class="o">=</span><span class="s2">&quot;stat&quot;</span><span class="p">,</span>
        <span class="n">href</span><span class="o">=</span><span class="s1">&#39;http://bowtie-bio.sourceforge.net/bowtie2/&#39;</span><span class="p">,</span>
        <span class="n">info</span><span class="o">=</span><span class="s2">&quot;is an ultrafast and memory-efficient tool for aligning sequencing&quot;</span>\
                <span class="s2">&quot; reads to long reference sequences.&quot;</span><span class="p">)</span>

        <span class="c1"># Find and load any Bowtie 2 reports</span>
        <span class="bp">self</span><span class="o">.</span><span class="n">bowtie2_data</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">()</span>
        <span class="bp">self</span><span class="o">.</span><span class="n">num_se</span> <span class="o">=</span> <span class="mi">0</span>
        <span class="bp">self</span><span class="o">.</span><span class="n">num_pe</span> <span class="o">=</span> <span class="mi">0</span>
        <span class="nb">print</span><span class="p">(</span><span class="nb">dir</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">find_log_files</span><span class="p">))</span>
        <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;&quot;</span><span class="p">)</span>
        <span class="nb">print</span><span class="p">(</span><span class="n">help</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">find_log_files</span><span class="p">))</span>
        <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">find_log_files</span><span class="p">(</span><span class="s1">&#39;mapping/flagstats&#39;</span><span class="p">,</span> <span class="n">filehandles</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
            <span class="bp">self</span><span class="o">.</span><span class="n">parse_bowtie2_logs</span><span class="p">(</span><span class="n">f</span><span class="p">)</span>

        <span class="c1"># Filter to strip out ignored sample names</span>
        <span class="bp">self</span><span class="o">.</span><span class="n">bowtie2_data</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ignore_samples</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bowtie2_data</span><span class="p">)</span>

        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bowtie2_data</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
            <span class="k">raise</span> <span class="ne">UserWarning</span>

        <span class="n">log</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">&quot;Found </span><span class="si">{}</span><span class="s2"> reports&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bowtie2_data</span><span class="p">)))</span>

        <span class="c1"># Write parsed report data to a file</span>
        <span class="bp">self</span><span class="o">.</span><span class="n">write_data_file</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bowtie2_data</span><span class="p">,</span> <span class="s1">&#39;multiqc_bowtie2&#39;</span><span class="p">)</span>

        <span class="c1"># Basic Stats Table</span>
        <span class="c1"># Report table is immutable, so just updating it works</span>
        <span class="bp">self</span><span class="o">.</span><span class="n">bowtie2_general_stats_table</span><span class="p">()</span>

        <span class="c1"># Alignment Rate Plot</span>
        <span class="bp">self</span><span class="o">.</span><span class="n">bowtie2_alignment_plot</span><span class="p">()</span>


    <span class="k">def</span> <span class="nf">parse_bowtie2_logs</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">f</span><span class="p">):</span>
        <span class="sd">&quot;&quot;&quot;</span>
<span class="sd">        Warning: This function may make you want to stab yourself.</span>
<span class="sd">        Parse logs from bowtie2. These miss several key bits of information</span>
<span class="sd">        such as input files, so we try to look for logs from other wrapper tools</span>
<span class="sd">        that may have logged this info. If not found, we default to using the filename.</span>
<span class="sd">        Note that concatenated logs only parse if we have the command printed in there.</span>
<span class="sd">        The bowtie log uses the same strings mulitple times in different contexts to mean</span>
<span class="sd">        different things, making parsing very messy. Handle with care.</span>
<span class="sd">        Example single-end output from bowtie2:</span>
<span class="sd">            Time loading reference: 00:00:08</span>
<span class="sd">            Time loading forward index: 00:00:16</span>
<span class="sd">            Time loading mirror index: 00:00:09</span>
<span class="sd">            [samopen] SAM header is present: 25 sequences.</span>
<span class="sd">            Multiseed full-index search: 00:58:04</span>
<span class="sd">            38377305 reads; of these:</span>
<span class="sd">              38377305 (100.00%) were unpaired; of these:</span>
<span class="sd">                2525577 (6.58%) aligned 0 times</span>
<span class="sd">                27593593 (71.90%) aligned exactly 1 time</span>
<span class="sd">                8258135 (21.52%) aligned &gt;1 times</span>
<span class="sd">            93.42% overall alignment rate</span>
<span class="sd">            Time searching: 00:58:37</span>
<span class="sd">            Overall time: 00:58:37</span>
<span class="sd">        Example paired-end output from bowtie2:</span>
<span class="sd">            Time loading reference: 00:01:07</span>
<span class="sd">            Time loading forward index: 00:00:26</span>
<span class="sd">            Time loading mirror index: 00:00:09</span>
<span class="sd">            Multiseed full-index search: 01:32:55</span>
<span class="sd">            15066949 reads; of these:</span>
<span class="sd">              15066949 (100.00%) were paired; of these:</span>
<span class="sd">                516325 (3.43%) aligned concordantly 0 times</span>
<span class="sd">                11294617 (74.96%) aligned concordantly exactly 1 time</span>
<span class="sd">                3256007 (21.61%) aligned concordantly &gt;1 times</span>
<span class="sd">                ----</span>
<span class="sd">                516325 pairs aligned concordantly 0 times; of these:</span>
<span class="sd">                  26692 (5.17%) aligned discordantly 1 time</span>
<span class="sd">                ----</span>
<span class="sd">                489633 pairs aligned 0 times concordantly or discordantly; of these:</span>
<span class="sd">                  979266 mates make up the pairs; of these:</span>
<span class="sd">                    592900 (60.55%) aligned 0 times</span>
<span class="sd">                    209206 (21.36%) aligned exactly 1 time</span>
<span class="sd">                    177160 (18.09%) aligned &gt;1 times</span>
<span class="sd">            98.03% overall alignment rate</span>
<span class="sd">            Time searching: 01:34:37</span>
<span class="sd">            Overall time: 01:34:37</span>
<span class="sd">        &quot;&quot;&quot;</span>

        <span class="c1"># Regexes</span>
        <span class="n">regexes</span> <span class="o">=</span> <span class="p">{</span>
            <span class="s1">&#39;unpaired&#39;</span><span class="p">:</span> <span class="p">{</span>
                <span class="s1">&#39;unpaired_aligned_none&#39;</span><span class="p">:</span> <span class="sa">r</span><span class="s2">&quot;(\d+) \([\d\.]+%\) aligned 0 times&quot;</span><span class="p">,</span>
                <span class="s1">&#39;unpaired_aligned_one&#39;</span><span class="p">:</span> <span class="sa">r</span><span class="s2">&quot;(\d+) \([\d\.]+%\) aligned exactly 1 time&quot;</span><span class="p">,</span>
                <span class="s1">&#39;unpaired_aligned_multi&#39;</span><span class="p">:</span> <span class="sa">r</span><span class="s2">&quot;(\d+) \([\d\.]+%\) aligned &gt;1 times&quot;</span>
            <span class="p">},</span>
            <span class="s1">&#39;paired&#39;</span><span class="p">:</span> <span class="p">{</span>
                <span class="s1">&#39;paired_aligned_none&#39;</span><span class="p">:</span> <span class="sa">r</span><span class="s2">&quot;(\d+) \([\d\.]+%\) aligned concordantly 0 times&quot;</span><span class="p">,</span>
                <span class="s1">&#39;paired_aligned_one&#39;</span><span class="p">:</span> <span class="sa">r</span><span class="s2">&quot;(\d+) \([\d\.]+%\) aligned concordantly exactly 1 time&quot;</span><span class="p">,</span>
                <span class="s1">&#39;paired_aligned_multi&#39;</span><span class="p">:</span> <span class="sa">r</span><span class="s2">&quot;(\d+) \([\d\.]+%\) aligned concordantly &gt;1 times&quot;</span><span class="p">,</span>
                <span class="s1">&#39;paired_aligned_discord_one&#39;</span><span class="p">:</span> <span class="sa">r</span><span class="s2">&quot;(\d+) \([\d\.]+%\) aligned discordantly 1 time&quot;</span><span class="p">,</span>
                <span class="s1">&#39;paired_aligned_discord_multi&#39;</span><span class="p">:</span> <span class="sa">r</span><span class="s2">&quot;(\d+) \([\d\.]+%\) aligned discordantly &gt;1 times&quot;</span><span class="p">,</span>
                <span class="s1">&#39;paired_aligned_mate_one&#39;</span><span class="p">:</span> <span class="sa">r</span><span class="s2">&quot;(\d+) \([\d\.]+%\) aligned exactly 1 time&quot;</span><span class="p">,</span>
                <span class="s1">&#39;paired_aligned_mate_multi&#39;</span><span class="p">:</span> <span class="sa">r</span><span class="s2">&quot;(\d+) \([\d\.]+%\) aligned &gt;1 times&quot;</span><span class="p">,</span>
                <span class="s1">&#39;paired_aligned_mate_none&#39;</span><span class="p">:</span> <span class="sa">r</span><span class="s2">&quot;(\d+) \([\d\.]+%\) aligned 0 times&quot;</span>
            <span class="p">}</span>
        <span class="p">}</span>

        <span class="c1"># Go through log file line by line</span>
        <span class="n">s_name</span> <span class="o">=</span> <span class="n">f</span><span class="p">[</span><span class="s1">&#39;s_name&#39;</span><span class="p">]</span>
        <span class="n">parsed_data</span> <span class="o">=</span> <span class="p">{}</span>

        <span class="k">for</span> <span class="n">l</span> <span class="ow">in</span> <span class="n">f</span><span class="p">[</span><span class="s1">&#39;f&#39;</span><span class="p">]:</span>
            <span class="c1"># Attempt in vain to find original bowtie2 command, logged by another program</span>
            <span class="n">btcmd</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="sa">r</span><span class="s2">&quot;bowtie2 .+ -[1U] ([^\s,]+)&quot;</span><span class="p">,</span> <span class="n">l</span><span class="p">)</span>
            <span class="k">if</span> <span class="n">btcmd</span><span class="p">:</span>
                <span class="n">s_name</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">clean_s_name</span><span class="p">(</span><span class="n">btcmd</span><span class="o">.</span><span class="n">group</span><span class="p">(</span><span class="mi">1</span><span class="p">),</span> <span class="n">f</span><span class="p">[</span><span class="s1">&#39;root&#39;</span><span class="p">])</span>
                <span class="n">log</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">&quot;Found a bowtie2 command, updating sample name to &#39;</span><span class="si">{}</span><span class="s2">&#39;&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">s_name</span><span class="p">))</span>

            <span class="c1"># Total reads</span>
            <span class="n">total</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="sa">r</span><span class="s2">&quot;(\d+) reads; of these:&quot;</span><span class="p">,</span> <span class="n">l</span><span class="p">)</span>
            <span class="k">if</span> <span class="n">total</span><span class="p">:</span>
                <span class="n">parsed_data</span><span class="p">[</span><span class="s1">&#39;total_reads&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">total</span><span class="o">.</span><span class="n">group</span><span class="p">(</span><span class="mi">1</span><span class="p">))</span>

            <span class="c1"># Single end reads</span>
            <span class="n">unpaired</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="sa">r</span><span class="s2">&quot;(\d+) \([\d\.]+%\) were unpaired; of these:&quot;</span><span class="p">,</span> <span class="n">l</span><span class="p">)</span>
            <span class="k">if</span> <span class="n">unpaired</span><span class="p">:</span>
                <span class="n">parsed_data</span><span class="p">[</span><span class="s1">&#39;unpaired_total&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">unpaired</span><span class="o">.</span><span class="n">group</span><span class="p">(</span><span class="mi">1</span><span class="p">))</span>
                <span class="bp">self</span><span class="o">.</span><span class="n">num_se</span> <span class="o">+=</span> <span class="mi">1</span>

                <span class="c1"># Do nested loop whilst we have this level of indentation</span>
                <span class="n">l</span> <span class="o">=</span> <span class="n">f</span><span class="p">[</span><span class="s1">&#39;f&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">readline</span><span class="p">()</span>
                <span class="k">while</span> <span class="n">l</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;    &#39;</span><span class="p">):</span>
                    <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">regexes</span><span class="p">[</span><span class="s1">&#39;unpaired&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
                        <span class="n">match</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="n">r</span><span class="p">,</span> <span class="n">l</span><span class="p">)</span>
                        <span class="k">if</span> <span class="n">match</span><span class="p">:</span>
                            <span class="n">parsed_data</span><span class="p">[</span><span class="n">k</span><span class="p">]</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">match</span><span class="o">.</span><span class="n">group</span><span class="p">(</span><span class="mi">1</span><span class="p">))</span>
                    <span class="n">l</span> <span class="o">=</span> <span class="n">f</span><span class="p">[</span><span class="s1">&#39;f&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">readline</span><span class="p">()</span>

            <span class="c1"># Paired end reads</span>
            <span class="n">paired</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="sa">r</span><span class="s2">&quot;(\d+) \([\d\.]+%\) were paired; of these:&quot;</span><span class="p">,</span> <span class="n">l</span><span class="p">)</span>
            <span class="k">if</span> <span class="n">paired</span><span class="p">:</span>
                <span class="n">parsed_data</span><span class="p">[</span><span class="s1">&#39;paired_total&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">paired</span><span class="o">.</span><span class="n">group</span><span class="p">(</span><span class="mi">1</span><span class="p">))</span>
                <span class="bp">self</span><span class="o">.</span><span class="n">num_pe</span> <span class="o">+=</span> <span class="mi">1</span>

                <span class="c1"># Do nested loop whilst we have this level of indentation</span>
                <span class="n">l</span> <span class="o">=</span> <span class="n">f</span><span class="p">[</span><span class="s1">&#39;f&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">readline</span><span class="p">()</span>
                <span class="k">while</span> <span class="n">l</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;    &#39;</span><span class="p">):</span>
                    <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">regexes</span><span class="p">[</span><span class="s1">&#39;paired&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
                        <span class="n">match</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="n">r</span><span class="p">,</span> <span class="n">l</span><span class="p">)</span>
                        <span class="k">if</span> <span class="n">match</span><span class="p">:</span>
                            <span class="n">parsed_data</span><span class="p">[</span><span class="n">k</span><span class="p">]</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">match</span><span class="o">.</span><span class="n">group</span><span class="p">(</span><span class="mi">1</span><span class="p">))</span>
                    <span class="n">l</span> <span class="o">=</span> <span class="n">f</span><span class="p">[</span><span class="s1">&#39;f&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">readline</span><span class="p">()</span>

            <span class="c1"># Overall alignment rate</span>
            <span class="n">overall</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="sa">r</span><span class="s2">&quot;([\d\.]+)</span><span class="si">% o</span><span class="s2">verall alignment rate&quot;</span><span class="p">,</span> <span class="n">l</span><span class="p">)</span>
            <span class="k">if</span> <span class="n">overall</span><span class="p">:</span>
                <span class="n">parsed_data</span><span class="p">[</span><span class="s1">&#39;overall_alignment_rate&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">overall</span><span class="o">.</span><span class="n">group</span><span class="p">(</span><span class="mi">1</span><span class="p">))</span>

                <span class="c1"># End of log section</span>
                <span class="c1"># Save half &#39;pairs&#39; of mate counts</span>
                <span class="n">m_keys</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;paired_aligned_mate_multi&#39;</span><span class="p">,</span> <span class="s1">&#39;paired_aligned_mate_none&#39;</span><span class="p">,</span> <span class="s1">&#39;paired_aligned_mate_one&#39;</span><span class="p">]</span>
                <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="n">m_keys</span><span class="p">:</span>
                    <span class="k">if</span> <span class="n">k</span> <span class="ow">in</span> <span class="n">parsed_data</span><span class="p">:</span>
                        <span class="n">parsed_data</span><span class="p">[</span><span class="s1">&#39;</span><span class="si">{}</span><span class="s1">_halved&#39;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">k</span><span class="p">)]</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">parsed_data</span><span class="p">[</span><span class="n">k</span><span class="p">])</span> <span class="o">/</span> <span class="mf">2.0</span>
                <span class="c1"># Save parsed data</span>
                <span class="k">if</span> <span class="n">s_name</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">bowtie2_data</span><span class="p">:</span>
                    <span class="n">log</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">&quot;Duplicate sample name found! Overwriting: </span><span class="si">{}</span><span class="s2">&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">s_name</span><span class="p">))</span>
                <span class="bp">self</span><span class="o">.</span><span class="n">add_data_source</span><span class="p">(</span><span class="n">f</span><span class="p">,</span> <span class="n">s_name</span><span class="p">)</span>
                <span class="bp">self</span><span class="o">.</span><span class="n">bowtie2_data</span><span class="p">[</span><span class="n">s_name</span><span class="p">]</span> <span class="o">=</span> <span class="n">parsed_data</span>
                <span class="c1"># Reset in case we find more in this log file</span>
                <span class="n">s_name</span> <span class="o">=</span> <span class="n">f</span><span class="p">[</span><span class="s1">&#39;s_name&#39;</span><span class="p">]</span>
                <span class="n">parsed_data</span> <span class="o">=</span> <span class="p">{}</span>


    <span class="k">def</span> <span class="nf">bowtie2_general_stats_table</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
        <span class="sd">&quot;&quot;&quot; Take the parsed stats from the Bowtie 2 report and add it to the</span>
<span class="sd">        basic stats table at the top of the report &quot;&quot;&quot;</span>

        <span class="n">headers</span> <span class="o">=</span> <span class="n">OrderedDict</span><span class="p">()</span>
        <span class="n">headers</span><span class="p">[</span><span class="s1">&#39;overall_alignment_rate&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span>
            <span class="s1">&#39;title&#39;</span><span class="p">:</span> <span class="s1">&#39;% Aligned&#39;</span><span class="p">,</span>
            <span class="s1">&#39;description&#39;</span><span class="p">:</span> <span class="s1">&#39;overall alignment rate&#39;</span><span class="p">,</span>
            <span class="s1">&#39;max&#39;</span><span class="p">:</span> <span class="mi">100</span><span class="p">,</span>
            <span class="s1">&#39;min&#39;</span><span class="p">:</span> <span class="mi">0</span><span class="p">,</span>
            <span class="s1">&#39;suffix&#39;</span><span class="p">:</span> <span class="s1">&#39;%&#39;</span><span class="p">,</span>
            <span class="s1">&#39;scale&#39;</span><span class="p">:</span> <span class="s1">&#39;YlGn&#39;</span>
        <span class="p">}</span>
        <span class="bp">self</span><span class="o">.</span><span class="n">general_stats_addcols</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bowtie2_data</span><span class="p">,</span> <span class="n">headers</span><span class="p">)</span>

    <span class="k">def</span> <span class="nf">bowtie2_alignment_plot</span> <span class="p">(</span><span class="bp">self</span><span class="p">):</span>
        <span class="sd">&quot;&quot;&quot; Make the HighCharts HTML to plot the alignment rates &quot;&quot;&quot;</span>

        <span class="n">half_warning</span> <span class="o">=</span> <span class="s1">&#39;&#39;</span>
        <span class="k">for</span> <span class="n">s_name</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">bowtie2_data</span><span class="p">:</span>
            <span class="k">if</span> <span class="s1">&#39;paired_aligned_mate_one_halved&#39;</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">bowtie2_data</span><span class="p">[</span><span class="n">s_name</span><span class="p">]</span> <span class="ow">or</span> <span class="s1">&#39;paired_aligned_mate_multi_halved&#39;</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">bowtie2_data</span><span class="p">[</span><span class="n">s_name</span><span class="p">]</span> <span class="ow">or</span> <span class="s1">&#39;paired_aligned_mate_none_halved&#39;</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">bowtie2_data</span><span class="p">[</span><span class="n">s_name</span><span class="p">]:</span>
                <span class="n">half_warning</span> <span class="o">=</span> <span class="s1">&#39;&lt;em&gt;Please note that single mate alignment counts are halved to tally with pair counts properly.&lt;/em&gt;&#39;</span>
        <span class="n">description_text</span> <span class="o">=</span> <span class="s1">&#39;This plot shows the number of reads aligning to the reference in different ways.&#39;</span>

        <span class="c1"># Config for the plot</span>
        <span class="n">config</span> <span class="o">=</span> <span class="p">{</span>
            <span class="s1">&#39;ylab&#39;</span><span class="p">:</span> <span class="s1">&#39;# Reads&#39;</span><span class="p">,</span>
            <span class="s1">&#39;cpswitch_counts_label&#39;</span><span class="p">:</span> <span class="s1">&#39;Number of Reads&#39;</span>
        <span class="p">}</span>

        <span class="c1"># Two plots, don&#39;t mix SE with PE</span>
        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">num_se</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">:</span>
            <span class="n">sekeys</span> <span class="o">=</span> <span class="n">OrderedDict</span><span class="p">()</span>
            <span class="n">sekeys</span><span class="p">[</span><span class="s1">&#39;unpaired_aligned_one&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span> <span class="s1">&#39;color&#39;</span><span class="p">:</span> <span class="s1">&#39;#20568f&#39;</span><span class="p">,</span> <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;SE mapped uniquely&#39;</span> <span class="p">}</span>
            <span class="n">sekeys</span><span class="p">[</span><span class="s1">&#39;unpaired_aligned_multi&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span> <span class="s1">&#39;color&#39;</span><span class="p">:</span> <span class="s1">&#39;#f7a35c&#39;</span><span class="p">,</span> <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;SE multimapped&#39;</span> <span class="p">}</span>
            <span class="n">sekeys</span><span class="p">[</span><span class="s1">&#39;unpaired_aligned_none&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span> <span class="s1">&#39;color&#39;</span><span class="p">:</span> <span class="s1">&#39;#981919&#39;</span><span class="p">,</span> <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;SE not aligned&#39;</span> <span class="p">}</span>
            <span class="n">config</span><span class="p">[</span><span class="s1">&#39;id&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s1">&#39;bowtie2_se_plot&#39;</span>
            <span class="n">config</span><span class="p">[</span><span class="s1">&#39;title&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s1">&#39;Bowtie 2: SE Alignment Scores&#39;</span>
            <span class="bp">self</span><span class="o">.</span><span class="n">add_section</span><span class="p">(</span>
                <span class="n">description</span> <span class="o">=</span> <span class="n">description_text</span><span class="p">,</span>
                <span class="n">helptext</span> <span class="o">=</span> <span class="s1">&#39;&#39;&#39;</span>
<span class="s1">                There are 3 possible types of alignment:</span>
<span class="s1">                * **SE Mapped uniquely**: Read has only one occurence in the reference genome.</span>
<span class="s1">                * **SE Multimapped**: Read has multiple occurence.</span>
<span class="s1">                * **SE No aligned**: Read has no occurence.</span>
<span class="s1">                &#39;&#39;&#39;</span><span class="p">,</span>
                <span class="n">plot</span> <span class="o">=</span> <span class="n">bargraph</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bowtie2_data</span><span class="p">,</span> <span class="n">sekeys</span><span class="p">,</span> <span class="n">config</span><span class="p">)</span>
            <span class="p">)</span>

        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">num_pe</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">:</span>
            <span class="n">pekeys</span> <span class="o">=</span> <span class="n">OrderedDict</span><span class="p">()</span>
            <span class="n">pekeys</span><span class="p">[</span><span class="s1">&#39;paired_aligned_one&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span> <span class="s1">&#39;color&#39;</span><span class="p">:</span> <span class="s1">&#39;#20568f&#39;</span><span class="p">,</span> <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;PE mapped uniquely&#39;</span> <span class="p">}</span>
            <span class="n">pekeys</span><span class="p">[</span><span class="s1">&#39;paired_aligned_discord_one&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span> <span class="s1">&#39;color&#39;</span><span class="p">:</span> <span class="s1">&#39;#5c94ca&#39;</span><span class="p">,</span> <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;PE mapped discordantly uniquely&#39;</span> <span class="p">}</span>
            <span class="n">pekeys</span><span class="p">[</span><span class="s1">&#39;paired_aligned_mate_one_halved&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span> <span class="s1">&#39;color&#39;</span><span class="p">:</span> <span class="s1">&#39;#95ceff&#39;</span><span class="p">,</span> <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;PE one mate mapped uniquely&#39;</span> <span class="p">}</span>
            <span class="n">pekeys</span><span class="p">[</span><span class="s1">&#39;paired_aligned_multi&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span> <span class="s1">&#39;color&#39;</span><span class="p">:</span> <span class="s1">&#39;#f7a35c&#39;</span><span class="p">,</span> <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;PE multimapped&#39;</span> <span class="p">}</span>
            <span class="n">pekeys</span><span class="p">[</span><span class="s1">&#39;paired_aligned_discord_multi&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span> <span class="s1">&#39;color&#39;</span><span class="p">:</span> <span class="s1">&#39;#dce333&#39;</span><span class="p">,</span> <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;PE discordantly multimapped&#39;</span> <span class="p">}</span>
            <span class="n">pekeys</span><span class="p">[</span><span class="s1">&#39;paired_aligned_mate_multi_halved&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span> <span class="s1">&#39;color&#39;</span><span class="p">:</span> <span class="s1">&#39;#ffeb75&#39;</span><span class="p">,</span> <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;PE one mate multimapped&#39;</span> <span class="p">}</span>
            <span class="n">pekeys</span><span class="p">[</span><span class="s1">&#39;paired_aligned_mate_none_halved&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span> <span class="s1">&#39;color&#39;</span><span class="p">:</span> <span class="s1">&#39;#981919&#39;</span><span class="p">,</span> <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;PE neither mate aligned&#39;</span> <span class="p">}</span>
            <span class="n">config</span><span class="p">[</span><span class="s1">&#39;id&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s1">&#39;bowtie2_pe_plot&#39;</span>
            <span class="n">config</span><span class="p">[</span><span class="s1">&#39;title&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s1">&#39;Bowtie 2: PE Alignment Scores&#39;</span>
            <span class="bp">self</span><span class="o">.</span><span class="n">add_section</span><span class="p">(</span>
                <span class="n">description</span> <span class="o">=</span> <span class="s2">&quot;&lt;br&gt;&quot;</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">description_text</span><span class="p">,</span><span class="n">half_warning</span><span class="p">]),</span>
                <span class="n">helptext</span> <span class="o">=</span> <span class="s1">&#39;&#39;&#39;</span>
<span class="s1">                There are 6 possible types of alignment:</span>
<span class="s1">                * **PE mapped uniquely**: Pair has only one occurence in the reference genome.</span>
<span class="s1">                * **PE mapped discordantly uniquely**: Pair has only one occurence but not in proper pair.</span>
<span class="s1">                * **PE one mate mapped uniquely**: One read of a pair has one occurence.</span>
<span class="s1">                * **PE multimapped**: Pair has multiple occurence.</span>
<span class="s1">                * **PE one mate multimapped**: One read of a pair has multiple occurence.</span>
<span class="s1">                * **PE neither mate aligned**: Pair has no occurence.</span>
<span class="s1">                &#39;&#39;&#39;</span><span class="p">,</span>
                <span class="n">plot</span> <span class="o">=</span> <span class="n">bargraph</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bowtie2_data</span><span class="p">,</span> <span class="n">pekeys</span><span class="p">,</span> <span class="n">config</span><span class="p">)</span>
            <span class="p">)</span>
</pre></div>

    </div>
</div>
</div>

  </div>

  
  <div class="
      cell border-box-sizing code_cell rendered">
    <div class="input">

<div class="inner_cell">
    <div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="c1"># fh = open(&quot;figures/metadata.html&quot;,&quot;w&quot;)</span>
<span class="c1"># fh.write(metadata.head(25).to_html())</span>
<span class="c1"># fh.close()</span>
<span class="c1">#A custom function to help us find the raw fastq files</span>
<span class="kn">from</span> <span class="nn">glob</span> <span class="k">import</span> <span class="n">glob</span>
<span class="n">rawFastqFiles</span> <span class="o">=</span> <span class="n">glob</span><span class="p">(</span><span class="s1">&#39;jgi_transfer/metaT_raw/*/Raw_Data/*&#39;</span><span class="p">)</span>

<span class="k">def</span> <span class="nf">lookupFSTQ</span><span class="p">(</span><span class="n">name</span><span class="p">,</span><span class="n">rawFastqFiles</span><span class="p">):</span>
    <span class="n">fastqName</span> <span class="o">=</span> <span class="s1">&#39;&#39;</span>
    <span class="n">found</span> <span class="o">=</span> <span class="kc">False</span>
    <span class="k">for</span> <span class="n">fastqName</span> <span class="ow">in</span> <span class="n">rawFastqFiles</span><span class="p">:</span>
        <span class="k">if</span> <span class="n">name</span> <span class="ow">in</span> <span class="n">fastqName</span><span class="p">:</span> 
            <span class="n">found</span> <span class="o">=</span> <span class="kc">True</span>
            <span class="k">break</span>
    <span class="k">if</span> <span class="n">found</span><span class="p">:</span>
        <span class="n">rawFastqFiles</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="n">fastqName</span><span class="p">)</span>
        <span class="k">return</span> <span class="n">fastqName</span>
</pre></div>

    </div>
</div>
</div>

  </div>


<!-- Loads nbinteract package -->
<script src="https://unpkg.com/nbinteract-core" async></script>
<script>
  (function setupNbinteract() {
    // If NbInteract hasn't loaded, wait one second and try again
    if (window.NbInteract === undefined) {
      setTimeout(setupNbinteract, 1000)
      return
    }

    var interact = new window.NbInteract({
      spec: 'skDooley/GLBRC/master',
      baseUrl: 'https://mybinder.org',
      provider: 'gh',
    })
    interact.prepare()

    window.interact = interact
  })()
</script>
    </div>
  </div>
</body>