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index.php
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<!DOCTYPE html>
<html>
<head>
<title>GeMo</title>
<meta charset="utf-8">
<!--Bootstrap 4.4-->
<link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.4.1/css/bootstrap.min.css" integrity="sha384-Vkoo8x4CGsO3+Hhxv8T/Q5PaXtkKtu6ug5TOeNV6gBiFeWPGFN9MuhOf23Q9Ifjh" crossorigin="anonymous">
<script src="https://ajax.googleapis.com/ajax/libs/jquery/3.5.1/jquery.min.js"></script>
<script src="https://cdn.jsdelivr.net/npm/popper.js@1.16.0/dist/umd/popper.min.js" integrity="sha384-Q6E9RHvbIyZFJoft+2mJbHaEWldlvI9IOYy5n3zV9zzTtmI3UksdQRVvoxMfooAo" crossorigin="anonymous"></script>
<script src="https://stackpath.bootstrapcdn.com/bootstrap/4.4.1/js/bootstrap.min.js" integrity="sha384-wfSDF2E50Y2D1uUdj0O3uMBJnjuUD4Ih7YwaYd1iqfktj0Uod8GCExl3Og8ifwB6" crossorigin="anonymous"></script>
<!-- <link href="https://stackpath.bootstrapcdn.com/bootswatch/4.4.1/sandstone/bootstrap.min.css" rel="stylesheet" integrity="sha384-ABdnjefqVzESm+f9z9hcqx2cvwvDNjfrwfW5Le9138qHCMGlNmWawyn/tt4jR4ba" crossorigin="anonymous"> -->
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/d3/4.1.1/d3.min.js"></script>
<!-- <script src="https://cdn.jsdelivr.net/npm/ideogram@1.16.0/dist/js/ideogram.min.js"></script> -->
<!-- <script src="https://cdn.jsdelivr.net/npm/ideogram@1.20.0/dist/js/ideogram.min.js"></script> -->
<!-- Ideogram -->
<!-- <script src="dist/ideogram/dist/js/ideogram.min.js"></script> -->
<script src="https://cdn.jsdelivr.net/npm/ideogram@1.31.0/dist/js/ideogram.min.js"></script>
<!--Tooltipster-->
<link rel="stylesheet" type="text/css" href="dist/tooltipster/dist/css/tooltipster.bundle.min.css" />
<link rel="stylesheet" type="text/css" href="dist/tooltipster/dist/css/plugins/tooltipster/sideTip/themes/tooltipster-sideTip-noir.min.css" />
<script type="text/javascript" src="dist/tooltipster/dist/js/tooltipster.bundle.min.js"></script>
<!--select2-->
<link href="https://cdn.jsdelivr.net/npm/select2@4.1.0-rc.0/dist/css/select2.min.css" rel="stylesheet" />
<script src="https://cdn.jsdelivr.net/npm/select2@4.1.0-rc.0/dist/js/select2.min.js"></script>
<!--gemo-->
<script type="module" src="src/main.js" defer></script>
<link rel="stylesheet" type="text/css" href="src/css/gemo.css">
<link rel="shortcut icon" href="/gemo/public/img/favicon.ico">
<!--chrompaint-->
<!-- <script type="module" src="src/chrompaint/main.js" defer></script> -->
<link href="src/css/chrompaint.css" rel="stylesheet">
<!--libs-->
<script type="text/javascript" src="src/html2canvas.js"></script>
<script type="text/javascript" src="src/canvas2image.js"></script>
<script type="module" src="https://cdn.jsdelivr.net/gh/zerodevx/zero-md@2/dist/zero-md.min.js"></script>
<script type="text/javascript" src="dist/jszip/jszip.min.js"></script>
<script type="text/javascript" src="dist/file-saver/FileSaver.min.js"></script>
<script src="https://d3js.org/colorbrewer.v1.min.js"></script>
<!--d3-->
<script src="https://d3js.org/d3-axis.v2.min.js"></script>
<!--SocketIO-->
<script src="node_modules/socket.io/client-dist/socket.io.js"></script>
<script>
// var socket = io('http://195.221.173.169:9070');
var socket = io('http://195.221.175.11:9070');
</script>
</head>
<body>
<!--JUMBOTRON-->
<div id="banner" class="jumbotron jumbo-bg">
<div class="row">
<div class="col col-home">
<p class="lead">
<img src="./public/img/GeMo_full.png"></img>
Genetic mosaicism painting
</p>
</div>
<div class="col col-icon" >
<div class="row">
<span class="helper"></span>
<p class="icon-legend">
<a href="https://github.com/SouthGreenPlatform/GeMo" target="_blank">
<img class="ghimg" src="./public/img/GitHub-Mark-Light-120px-plus.png"></img>
</a>
</p>
</div>
<div class="row">
<p class="icon-legend" >Github</p>
</div>
</div>
<div class="col col-icon" ">
<div class="row">
<span class="helper"></span>
<p class="icon-legend">
<a href="https://gemo.readthedocs.io/en/latest/" target="_blank">
<img class="ghimg" src="./public/img/logo-light.svg"></img>
</a>
</p>
</div>
<div class="row">
<p class="icon-legend" >Read The Docs</p>
</div>
</div>
</div>
</div>
<!-- END OF JUMBOTRON-->
<div id="loader" class="triple-spinner" style="display:none;"></div>
<?php
//echo json_encode(file_get_contents($_POST["data"]));
//echo $_POST["select"];
if(isset($_FILES["data"])){
$data = json_encode(file_get_contents($_FILES["data"]["tmp_name"]));
$ploidyPost = $_POST["select"];
echo "<script>
config.ploidy = $ploidyPost;
$(\"#selectorploidy\").val('$ploidyPost');
var datajs = {$data};
datajs = datajs.substring(0, datajs.length-1);
console.log(datajs);
load_post_file(datajs);
</script>";
if(!empty($_FILES["annot"])){
$annot = json_encode(file_get_contents($_FILES["annot"]["tmp_name"]));
echo "<script>
var annotjs = {$annot};
annotjs = annotjs.substring(0, annotjs.length-1);
console.log(annotjs);
annotationParser(annotjs);
//</script>";
}
echo "<script> load_ideogram()</script>";
}
elseif(isset($_POST["data"])){
$data = json_encode(file_get_contents($_POST["data"]));
$ploidyPost = $_POST["select"];
echo "<script>
config.ploidy = $ploidyPost;
$(\"#selectorploidy\").val('$ploidyPost');
var datajs = {$data};
datajs = datajs.substring(0, datajs.length-1);
$(\"#editorChr\").text(datajs);
</script>";
if(!empty($_POST["annot"])){
$annot = json_encode(file_get_contents($_POST["annot"]));
echo "<script>
var annotjs = {$annot};
annotjs = annotjs.substring(0, annotjs.length-1);
console.log(annotjs);
$(\"#editorAnnot\").text(annotjs);
//</script>";
}
echo "<script> load_ideogram()</script>";
}
?>
<!--SIDEBAR-->
<div id="wrapper">
<div id="sidebar-wrapper">
<aside id="sidebar">
<ul id="sidemenu" class="sidebar-nav">
<!--HOME-->
<li id="homebutton">
<a class="accordion-toggle collapsed toggle-switch" data-toggle="collapse" href="#submenu-1">
<span class="sidebar-icon"><i class="fa fa-dashboard"></i></span>
<span class="sidebar-title">Home</span>
<b class="caret"></b>
</a>
<!-- <ul id="submenu-1" class="panel-collapse collapse panel-switch" role="menu">
</ul> -->
</li>
<!--ACCESSION-->
<li id="accession">
<a class="accordion-toggle toggle-switch" data-toggle="collapse" href="#submenu-2">
<span class="sidebar-icon"><i class="fa fa-dashboard"></i></span>
<span class="sidebar-title">Chromosome Painting</span>
<b class="caret"></b>
</a>
<ul id="submenu-2" class="panel-collapse collapse panel-switch show" role="menu">
<!-- Menu-->
<li>
<div class="form-group">
<!-- bloc or curve -->
<!-- <p class="menu_title">
Choose your visualization type
<svg xmlns="http://www.w3.org/2000/svg" cursor="pointer" width="16" height="16" fill="currentColor" class="bi bi-question-circle blocOrCurve" viewBox="0 0 16 16">
<path d="M8 15A7 7 0 1 1 8 1a7 7 0 0 1 0 14zm0 1A8 8 0 1 0 8 0a8 8 0 0 0 0 16z"/>
<path d="M5.255 5.786a.237.237 0 0 0 .241.247h.825c.138 0 .248-.113.266-.25.09-.656.54-1.134 1.342-1.134.686 0 1.314.343 1.314 1.168 0 .635-.374.927-.965 1.371-.673.489-1.206 1.06-1.168 1.987l.003.217a.25.25 0 0 0 .25.246h.811a.25.25 0 0 0 .25-.25v-.105c0-.718.273-.927 1.01-1.486.609-.463 1.244-.977 1.244-2.056 0-1.511-1.276-2.241-2.673-2.241-1.267 0-2.655.59-2.75 2.286zm1.557 5.763c0 .533.425.927 1.01.927.609 0 1.028-.394 1.028-.927 0-.552-.42-.94-1.029-.94-.584 0-1.009.388-1.009.94z"/>
</svg>
</p>
<div class="btn-group btn-group-toggle" id="radio_form" data-toggle="buttons">
<label class="myradiobtn btn btn-sm btn-outline-dark active">
<input type="radio" name="formchoice" id="radioblock" value="block" autocomplete="off" checked> Mosaïc blocks (ideogram)
</label>
<label class="myradiobtn btn btn-sm btn-outline-dark">
<input type="radio" name="formchoice" id="radiocurve" value="curve" autocomplete="off"> Data curation (graph)
</label>
</div> -->
<!--Pre-loaded data-->
<div class="menu_division">
<p class="menu_title">
Pre-loaded examples
<svg xmlns="http://www.w3.org/2000/svg" cursor="pointer" width="16" height="16" fill="currentColor" class="bi bi-question-circle preloaded" viewBox="0 0 16 16">
<path d="M8 15A7 7 0 1 1 8 1a7 7 0 0 1 0 14zm0 1A8 8 0 1 0 8 0a8 8 0 0 0 0 16z"/>
<path d="M5.255 5.786a.237.237 0 0 0 .241.247h.825c.138 0 .248-.113.266-.25.09-.656.54-1.134 1.342-1.134.686 0 1.314.343 1.314 1.168 0 .635-.374.927-.965 1.371-.673.489-1.206 1.06-1.168 1.987l.003.217a.25.25 0 0 0 .25.246h.811a.25.25 0 0 0 .25-.25v-.105c0-.718.273-.927 1.01-1.486.609-.463 1.244-.977 1.244-2.056 0-1.511-1.276-2.241-2.673-2.241-1.267 0-2.655.59-2.75 2.286zm1.557 5.763c0 .533.425.927 1.01.927.609 0 1.028-.394 1.028-.927 0-.552-.42-.94-1.029-.94-.584 0-1.009.388-1.009.94z"/>
</svg>
</p>
<select class="custom-select custom-select-sm" id="organism">
<option value="Organism">--Organism--</option>
</select>
<select class="custom-select custom-select-sm chosen-select" id="sample">
<option value="Sample">Sample</option>
</select>
</div>
<!--Custom data-->
<p class="menu_title">
With your own data
<svg xmlns="http://www.w3.org/2000/svg" cursor="pointer" width="16" height="16" fill="currentColor" class="bi bi-question-circle yourdata" viewBox="0 0 16 16">
<path d="M8 15A7 7 0 1 1 8 1a7 7 0 0 1 0 14zm0 1A8 8 0 1 0 8 0a8 8 0 0 0 0 16z"/>
<path d="M5.255 5.786a.237.237 0 0 0 .241.247h.825c.138 0 .248-.113.266-.25.09-.656.54-1.134 1.342-1.134.686 0 1.314.343 1.314 1.168 0 .635-.374.927-.965 1.371-.673.489-1.206 1.06-1.168 1.987l.003.217a.25.25 0 0 0 .25.246h.811a.25.25 0 0 0 .25-.25v-.105c0-.718.273-.927 1.01-1.486.609-.463 1.244-.977 1.244-2.056 0-1.511-1.276-2.241-2.673-2.241-1.267 0-2.655.59-2.75 2.286zm1.557 5.763c0 .533.425.927 1.01.927.609 0 1.028-.394 1.028-.927 0-.552-.42-.94-1.029-.94-.584 0-1.009.388-1.009.94z"/>
</svg>
</p>
<!--type of data-->
<div class="menu_division">
<p class="menu_title">
<a id="title_form" data-toggle="collapse" href="#collapseInput" aria-expanded="false" aria-controls="collapseExample">
Input files
</a>
<svg xmlns="http://www.w3.org/2000/svg" cursor="pointer" width="16" height="16" fill="currentColor" class="bi bi-question-circle input" viewBox="0 0 16 16">
<path d="M8 15A7 7 0 1 1 8 1a7 7 0 0 1 0 14zm0 1A8 8 0 1 0 8 0a8 8 0 0 0 0 16z"/>
<path d="M5.255 5.786a.237.237 0 0 0 .241.247h.825c.138 0 .248-.113.266-.25.09-.656.54-1.134 1.342-1.134.686 0 1.314.343 1.314 1.168 0 .635-.374.927-.965 1.371-.673.489-1.206 1.06-1.168 1.987l.003.217a.25.25 0 0 0 .25.246h.811a.25.25 0 0 0 .25-.25v-.105c0-.718.273-.927 1.01-1.486.609-.463 1.244-.977 1.244-2.056 0-1.511-1.276-2.241-2.673-2.241-1.267 0-2.655.59-2.75 2.286zm1.557 5.763c0 .533.425.927 1.01.927.609 0 1.028-.394 1.028-.927 0-.552-.42-.94-1.029-.94-.584 0-1.009.388-1.009.94z"/>
</svg>
</p>
<div id="switch" style="display: none;" class="custom-control custom-switch">
<input type="checkbox" class="custom-control-input" id="Switch">
<label class="custom-control-label" for="Switch">Curve based mode</label>
</div>
<div id="smooth" class="custom-control custom-switch">
<input type="checkbox" class="custom-control-input" id="Smooth">
<label class="custom-control-label" for="Smooth">Smooth mode</label>
</div> -->
<!-- data-->
<div class="collapse" id="collapseInput">
<form class="my-form">
<textarea id="editorAnnot" rows="3" class="form-control" placeholder="Insert values here" ></textarea>
<div class="custom-file" style="width:90%;">
<input type="file" class="custom-file-input" id="dataFile" accept=".txt, .csv, .tab, .tsv">
<label class="custom-file-label" for="dataFile">Choose file</label>
</div>
</form>
</div>
</div>
<div class="menu_division">
<!--Chrom length data-->
<div>
<form class="my-form">
<p class="menu_title">
<a id="title_form" data-toggle="collapse" href="#collapseChr" aria-expanded="false" aria-controls="collapseExample">
Chromosomes size and labels
</a>
<svg xmlns="http://www.w3.org/2000/svg" cursor="pointer" width="16" height="16" fill="currentColor" class="bi bi-question-circle chrom" viewBox="0 0 16 16">
<path d="M8 15A7 7 0 1 1 8 1a7 7 0 0 1 0 14zm0 1A8 8 0 1 0 8 0a8 8 0 0 0 0 16z"/>
<path d="M5.255 5.786a.237.237 0 0 0 .241.247h.825c.138 0 .248-.113.266-.25.09-.656.54-1.134 1.342-1.134.686 0 1.314.343 1.314 1.168 0 .635-.374.927-.965 1.371-.673.489-1.206 1.06-1.168 1.987l.003.217a.25.25 0 0 0 .25.246h.811a.25.25 0 0 0 .25-.25v-.105c0-.718.273-.927 1.01-1.486.609-.463 1.244-.977 1.244-2.056 0-1.511-1.276-2.241-2.673-2.241-1.267 0-2.655.59-2.75 2.286zm1.557 5.763c0 .533.425.927 1.01.927.609 0 1.028-.394 1.028-.927 0-.552-.42-.94-1.029-.94-.584 0-1.009.388-1.009.94z"/>
</svg>
</p>
<div class="collapse" id="collapseChr">
<select class="custom-select custom-select-sm select_chrom" id="chromosomes">
<option value="Chrom">Choose organism</option>
</select>
<br/><br/>
or upload your own
<textarea id="editorChr" rows="3" class="form-control" placeholder="Insert values here" ></textarea>
<div class="custom-file" style="width:90%;">
<input type="file" class="custom-file-input" id="lenFile" accept=".txt, .csv, .tab, .tsv">
<label class="custom-file-label" for="lenFile">Choose file</label>
</div>
<!--Ploidy-->
<br/>
<br/>
<label for="selectorploidy">Global ploidy</label>
<select name="select" id="selectorploidy" class="custom-select-sm">
<option value="1">1</option>
<option value="2" selected>2</option>
<option value="3">3</option>
<option value="4">4</option>
</select>
<!--Letters show / hide-->
<div class="custom-control custom-switch">
<input type="checkbox" class="custom-control-input" id="SwitchLetters" checked ">
<label class="custom-control-label" for="SwitchLetters">Show Labels</label>
</div>
</div>
</form>
</div>
</div>
<!--Colors data-->
<div class="menu_division">
<form class="my-form">
<p class="menu_title">
<a id="title_form" data-toggle="collapse" href="#collapseColor" aria-expanded="false" aria-controls="collapseExample">
Colors (optional)
</a>
<svg xmlns="http://www.w3.org/2000/svg" cursor="pointer" width="16" height="16" fill="currentColor" class="bi bi-question-circle colors" viewBox="0 0 16 16">
<path d="M8 15A7 7 0 1 1 8 1a7 7 0 0 1 0 14zm0 1A8 8 0 1 0 8 0a8 8 0 0 0 0 16z"/>
<path d="M5.255 5.786a.237.237 0 0 0 .241.247h.825c.138 0 .248-.113.266-.25.09-.656.54-1.134 1.342-1.134.686 0 1.314.343 1.314 1.168 0 .635-.374.927-.965 1.371-.673.489-1.206 1.06-1.168 1.987l.003.217a.25.25 0 0 0 .25.246h.811a.25.25 0 0 0 .25-.25v-.105c0-.718.273-.927 1.01-1.486.609-.463 1.244-.977 1.244-2.056 0-1.511-1.276-2.241-2.673-2.241-1.267 0-2.655.59-2.75 2.286zm1.557 5.763c0 .533.425.927 1.01.927.609 0 1.028-.394 1.028-.927 0-.552-.42-.94-1.029-.94-.584 0-1.009.388-1.009.94z"/>
</svg>
</p>
<div class="collapse" id="collapseColor">
<p class="menu_title">
<a class="btn btn-sm btn-outline-dark" id="title_form_2" data-toggle="collapse" href="#palette" aria-expanded="false" aria-controls="palette">
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or enter your own color data
<textarea id="editorColor" rows="3" class="form-control" placeholder="Insert values here" ></textarea>
<div class="custom-file" style="width:90%;">
<input type="file" class="custom-file-input" id="colorFile" accept=".txt, .conf, .csv, .tab, .tsv">
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</div>
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<!--Bed data-->
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<form class="my-form">
<p class="menu_title">
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Annotations (optional)
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<svg xmlns="https://www.w3.org/2000/svg" cursor="pointer" width="16" height="16" fill="currentColor" class="bi bi-question-circle bed" viewBox="0 0 16 16">
<path d="M8 15A7 7 0 1 1 8 1a7 7 0 0 1 0 14zm0 1A8 8 0 1 0 8 0a8 8 0 0 0 0 16z"/>
<path d="M5.255 5.786a.237.237 0 0 0 .241.247h.825c.138 0 .248-.113.266-.25.09-.656.54-1.134 1.342-1.134.686 0 1.314.343 1.314 1.168 0 .635-.374.927-.965 1.371-.673.489-1.206 1.06-1.168 1.987l.003.217a.25.25 0 0 0 .25.246h.811a.25.25 0 0 0 .25-.25v-.105c0-.718.273-.927 1.01-1.486.609-.463 1.244-.977 1.244-2.056 0-1.511-1.276-2.241-2.673-2.241-1.267 0-2.655.59-2.75 2.286zm1.557 5.763c0 .533.425.927 1.01.927.609 0 1.028-.394 1.028-.927 0-.552-.42-.94-1.029-.94-.584 0-1.009.388-1.009.94z"/>
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<textarea id="editorBed" rows="3" class="form-control" placeholder="Insert values here" ></textarea>
<div class="custom-file" style="width:90%;">
<input type="file" class="custom-file-input" id="bedFile" >
<label class="custom-file-label" for="bedFile" id="bedLabel" >Choose file</label>
</div>
</div>
</form>
</div>
<!--Genome browser link data-->
<div class="menu_division">
<form class="my-form">
<p class="menu_title">
<a id="title_form" data-toggle="collapse" href="#collapseGB" aria-expanded="false" aria-controls="collapseExample">
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</a>
<svg xmlns="http://www.w3.org/2000/svg" cursor="pointer" width="16" height="16" fill="currentColor" class="bi bi-question-circle gb" viewBox="0 0 16 16">
<path d="M8 15A7 7 0 1 1 8 1a7 7 0 0 1 0 14zm0 1A8 8 0 1 0 8 0a8 8 0 0 0 0 16z"/>
<path d="M5.255 5.786a.237.237 0 0 0 .241.247h.825c.138 0 .248-.113.266-.25.09-.656.54-1.134 1.342-1.134.686 0 1.314.343 1.314 1.168 0 .635-.374.927-.965 1.371-.673.489-1.206 1.06-1.168 1.987l.003.217a.25.25 0 0 0 .25.246h.811a.25.25 0 0 0 .25-.25v-.105c0-.718.273-.927 1.01-1.486.609-.463 1.244-.977 1.244-2.056 0-1.511-1.276-2.241-2.673-2.241-1.267 0-2.655.59-2.75 2.286zm1.557 5.763c0 .533.425.927 1.01.927.609 0 1.028-.394 1.028-.927 0-.552-.42-.94-1.029-.94-.584 0-1.009.388-1.009.94z"/>
</svg>
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<div class="collapse" id="collapseGB">
<select class="custom-select custom-select-sm select_gb" id="gb">
<option value="gb">Choose genome browser</option>
</select>
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or enter your own
<input id="editorGB" type="text" class="form-control" placeholder="Insert values here">
</div>
</form>
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<!-- Update -->
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<div>
<!--Download image-->
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<!--Save as url-->
<button id="saveasurl" class="btn btn-sm btn-outline-dark">Save as url</button>
<!-- The text field -->
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<div class="saveAsURL" style="display: none;">
<input id="url" type="text" class="form-control form-control-sm" >
<!-- The button used to copy the text -->
<button id="copy" class="btn btn-sm btn-outline-dark">Copy</button>
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</li>
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</li>
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</aside>
</div>
<!-- fin de la sidebar -->
<!-- legende flottante -->
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<button type="button" class="btn btn-dark btn-sm" style="display: none" id="legend_button" data-toggle="collapse" data-target="#legend_div" aria-expanded="false" aria-controls="legend_div">
Legend
</button>
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<!-- fin legende flottante -->
<div id="home" class="container">
<div id="welcome">
<!--JUMBOTRON-->
<div class="jumbotron jb_welcome">
<h1 class="display-2">Welcome to GeMo</h1><br/>
</div>
</div> <!--fin du jumbotron-->
<div id="help-container"></div>
</div><!--fin du home-->
<div id="page-content-wrapper" role="main" class="ideo_container">
<!-- The ideogram goes here. -->
</div>
<div id="chrompaint" style="display: none">
<div id="box3">
<div id="graph"></div>
<div id="selector">
<div id="floorContainer">
</div>
</div>
</div>
<div id="box4">
</div>
<!-- fin chrompaint -->
</div>
</div>
<div class="tooltip_templates" >
<span class="help_content" id="tooltip_blocOrCurve">
<pre>
Mosaic visualization shows colored blocs on the chromosomes:
<img class="tooltip_img" src="./public/img/bloc.png"></img>
Data curation displays the ancestral components along the chromosomes
on an interactive graph to help the mosaïc construction:
<img class="tooltip_img" src="./public/img/curve.png"></img>
<pre>
</span>
</div>
<div class="tooltip_templates" >
<span class="help_content" id="tooltip_preloaded">
<pre>
Preloaded data from published studies or generated with VCFHunter or TraceAncestor.
<pre>
</span>
</div>
<div class="tooltip_templates" >
<span class="help_content" id="tooltip_your_data">
<pre>
Generate a visualization with your custom chromosomes data.
<pre>
</span>
</div>
<div class="tooltip_templates" >
<span class="help_content" id="tooltip_help">
<pre>
Chromosome data format, each column tab separated
chr, len, centromereInf (optional), centromereSup (optional), label (optional)
example :
chr len centromereInf centromereSup label
chr01 37945898 AB
chr02 34728925 11000000 AB
chr03 40528553 15000000 AB
chr04 44598304 13000000 22000000 AB
chr05 46248384 23000000 26000000 AB
chr06 42818424 23000000 27000000 AB
chr07 38870123 20000000 23000000 AB
chr08 50124231 21000000 25000000 AB
chr09 47435180 25000000 29000000 AB
chr10 39038070 12000000 16000000 AB
chr11 34441343 15000000 20000000 AB
<pre>
</span>
</div>
<div class="tooltip_templates" >
<div class="help_content" id="tooltip_input">
<span class="help_content" ">
<pre>
Enter a block file to display the mosaïc visualization :
chr haplotype start end ancestral_group
01 0 1 29070452 g4
01 1 1 29070452 g4
02 0 1 29511734 g4
02 1 1 29511734 g4
<img class="tooltip_img" src="./public/img/bloc.png"></img>
Enter a file containing the ancestral components along the chromosomes to display an interactive graph
and generate a new mosaïc visualisation :
chr start end V T S
chr01 1145 189582 0.001671983513048138 0.014082301923852172 0.0016386866759508464
chr01 189593 356965 0.0012441961973068657 0.012867234592909085 0.0018101312755326665
chr01 356968 488069 0.0011179557674005532 0.010035172902205201 0.000759432489203596
chr01 488097 633373 0.002678217164025965 0.010470727908771585 0.003896031529700906
<img class="tooltip_img" src="./public/img/curve.png"></img>
Generating datasets
In order to generate ready-to-use datasets, analyses can be conducted with the following software:
* VCFHunter
VCFHunter is a suite of python scripts enabling chromosome painting of indivisual based on the contribution
of ancestral groups using VCF files.
Please look at the tutorial:
https://github.com/SouthGreenPlatform/VcfHunter/blob/master/turorial_painting_GEMO_visualization.md
* TraceAncestor
TraceAncestor permits to estimate the allelic dosage of ancestral alleles in hybrid individuals and then
to perform chromosom painting.
Please look at the tutorial:
https://github.com/SouthGreenPlatform/TraceAncestor_gemo
<pre>
</span>
</div>
</div>
<div class="tooltip_templates" >
<div class="help_content" id="tooltip_colors">
<span class="help_content" ">
<pre>
group name hex
un undef_group #b4b4b4
g6 group6 #c00000
g5 group5 #9a029a
g3 group3 #1440cd
g2 group2 #ffc000
g1 group1 #000000
g4 group4 #00b009
g7 group7 #b4b4b4
g0 group0 #000000
<pre>
</span>
</div>
</div>
<div class="tooltip_templates" >
<div class="help_content" id="tooltip_bed">
<span class="help_content" id="tooltip_bed">
<pre>
bed file example :
chr01 5287838 5289224 gene 0 -
chr01 15485703 15486813 gene 0 +
chr01 15490016 15492587 gene 0 +
chr02 2276353 2277821 gene 0 +
chr02 15358393 15361764 gene 0 +
<pre>
</span>
</div>
</div>
<div class="tooltip_templates" >
<div class="help_content" id="tooltip_gb">
<span class="help_content" id="tooltip_gb">
<pre>
Jbrowse link example :
https://banana-genome-hub.southgreen.fr/content/m-acuminata-dh-pahang-version-2/
GeMo will generate tooltips when hovering over each chromosomal block.
A link is displayed to explore a chromosome block directly on jbrowse.
<img class="tooltip_img" src="./public/img/tooltip.png"></img>
The mosaic data are sent as tracks to be viewed in jbrowse.
<img class="tooltip_img" src="./public/img/jbrowse.png"></img>
<pre>
</span>
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