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index.php
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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
<head>
<link rel="icon" href="favicon.ico" type="image/ico" sizes="32x32">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<title>locBLAST - Local NCBI BLAST+ Search</title>
<link href="style.css" rel="stylesheet" type="text/css" />
<script type="text/javascript">//<![CDATA[
window.onload = function() {
document.getElementById('pgm_desc').innerHTML = "<a href='blastp.php'>⇐ Compares Protein Query vs Protein Database</a>";
//document.getElementById('tips').innerHTML = "Choose Program to Use and Database to Search";
document.getElementById('advsearch').disabled = true;
document.getElementById('blastp_program').style.visibility = 'visible';
document.getElementById('datalib').getElementsByTagName("option")[0].disabled = false;
document.getElementById('datalib').getElementsByTagName("option")[1].disabled = false;
document.getElementById('datalib').getElementsByTagName("option")[2].disabled = false;
document.getElementById('datalib').getElementsByTagName("option")[3].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[4].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[5].disabled = false;
document.getElementById('datalib').getElementsByTagName("option")[6].disabled = false;
document.getElementById('datalib').getElementsByTagName("option")[7].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[8].disabled = false;
document.getElementById('datalib').getElementsByTagName("option")[9].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[10].disabled = false;
document.getElementById('datalib').getElementsByTagName("option")[0].selected = true;
};
function download_fasta(db, entry, acc_no, title, frm, to, seq) {
var xhttp = new XMLHttpRequest();
var params = "db=" + db + "&entry=" + entry + "&acc_no=" + acc_no + "&title=" + title + "&frm=" + frm + "&to=" + to + "&seq=" + seq;
xhttp.open('POST', 'download.php', true);
xhttp.setRequestHeader("Content-type", "application/x-www-form-urlencoded");
xhttp.setRequestHeader("Content-length", params.length);
xhttp.setRequestHeader("Connection", "close");
xhttp.send(params);
xhttp.onreadystatechange = function() {
if (this.readyState == 4 && this.status == 200) {
var hiddenElement = document.createElement('a');
hiddenElement.href = 'data:text/fasta;charset=utf-8,' + encodeURIComponent(this.responseText);
hiddenElement.target = '_blank';
hiddenElement.download = acc_no + ".fasta";
hiddenElement.click();
}
};
}
function blastUpdate() {
var request = new XMLHttpRequest();
request.onreadystatechange = function() {
if (this.readyState == 4 && this.status == 200) {
document.getElementById('update_msg').innerHTML = this.responseText;
} else {
document.getElementById('update_msg').innerHTML = '<div id="loading"></div>';
}
};
request.open('POST', 'update.php', true);
request.send();
}
function prgmDesc() {
var program = document.getElementById("program").value;
if (program == "blastn") {
document.getElementById('pgm_desc').innerHTML = "<a href='" + program + ".php'>⇐ Compares Nucleotide Query vs Nucleotide Database</a>";
document.getElementById('blastn_program').style.display = "block";
document.getElementById('datalib').getElementsByTagName("option")[0].disabled = false;
document.getElementById('datalib').getElementsByTagName("option")[1].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[2].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[3].disabled = false;
document.getElementById('datalib').getElementsByTagName("option")[4].disabled = false;
document.getElementById('datalib').getElementsByTagName("option")[5].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[6].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[7].disabled = false;
document.getElementById('datalib').getElementsByTagName("option")[8].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[9].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[10].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[0].selected = true;
document.getElementById("outfmt16").checked = true;
document.getElementById("outfmt16").disabled = false;
} else {
document.getElementById('blastn_program').style.display = "none";
}
if (program == "blastp") {
document.getElementById('pgm_desc').innerHTML = "<a href='" + program + ".php'>⇐ Compares Protein Query vs Protein Database</a>";
document.getElementById('blastp_program').style.display = "block";
document.getElementById('datalib').getElementsByTagName("option")[0].disabled = false;
document.getElementById('datalib').getElementsByTagName("option")[1].disabled = false;
document.getElementById('datalib').getElementsByTagName("option")[2].disabled = false;
document.getElementById('datalib').getElementsByTagName("option")[3].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[4].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[5].disabled = false;
document.getElementById('datalib').getElementsByTagName("option")[6].disabled = false;
document.getElementById('datalib').getElementsByTagName("option")[7].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[8].disabled = false;
document.getElementById('datalib').getElementsByTagName("option")[9].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[10].disabled = false;
document.getElementById('datalib').getElementsByTagName("option")[0].selected = true;
document.getElementById("outfmt16").checked = true;
document.getElementById("outfmt16").disabled = false;
} else {
document.getElementById('blastp_program').style.display = "none";
}
if (program == "blastx") {
document.getElementById('pgm_desc').innerHTML = "<a href='" + program + ".php'>⇐ Compares Nucleotide Query vs Protein Database</a>";
document.getElementById('blastx_program').style.display = "block";
document.getElementById('datalib').getElementsByTagName("option")[0].disabled = false;
document.getElementById('datalib').getElementsByTagName("option")[1].disabled = false;
document.getElementById('datalib').getElementsByTagName("option")[2].disabled = false;
document.getElementById('datalib').getElementsByTagName("option")[3].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[4].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[5].disabled = false;
document.getElementById('datalib').getElementsByTagName("option")[6].disabled = false;
document.getElementById('datalib').getElementsByTagName("option")[7].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[8].disabled = false;
document.getElementById('datalib').getElementsByTagName("option")[9].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[10].disabled = false;
document.getElementById('datalib').getElementsByTagName("option")[0].selected = true;
document.getElementById("outfmt16").checked = true;
document.getElementById("outfmt16").disabled = false;
} else {
document.getElementById('blastx_program').style.display = "none";
}
if (program == "tblastn") {
document.getElementById('pgm_desc').innerHTML = "<a href='" + program + ".php'>⇐ Compares Protein Query vs Nucleotide Database</a>";
document.getElementById('tblastn_program').style.display = "block";
document.getElementById('datalib').getElementsByTagName("option")[0].disabled = false;
document.getElementById('datalib').getElementsByTagName("option")[1].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[2].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[3].disabled = false;
document.getElementById('datalib').getElementsByTagName("option")[4].disabled = false;
document.getElementById('datalib').getElementsByTagName("option")[5].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[6].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[7].disabled = false;
document.getElementById('datalib').getElementsByTagName("option")[8].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[9].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[10].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[0].selected = true;
document.getElementById("outfmt16").checked = true;
document.getElementById("outfmt16").disabled = false;
} else {
document.getElementById('tblastn_program').style.display = "none";
}
if (program == "tblastx") {
document.getElementById('pgm_desc').innerHTML = "<a href='" + program + ".php'>⇐ Compares Nucleotide Query vs Nucleotide Database</a>";
document.getElementById('tblastx_program').style.display = "block";
document.getElementById('datalib').getElementsByTagName("option")[0].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[1].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[2].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[3].disabled = false;
document.getElementById('datalib').getElementsByTagName("option")[4].disabled = false;
document.getElementById('datalib').getElementsByTagName("option")[5].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[6].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[7].disabled = false;
document.getElementById('datalib').getElementsByTagName("option")[8].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[9].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[10].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[4].selected = true;
document.getElementById("outfmt16").checked = true;
document.getElementById("outfmt16").disabled = false;
} else {
document.getElementById('tblastx_program').style.display = "none";
}
if (program == "deltablast") {
document.getElementById('pgm_desc').innerHTML = "<a href='" + program + ".php'>⇐ Compares Protein Query vs Protein CD Database</a>";
document.getElementById('deltablast_program').style.display = "block";
document.getElementById('datalib').getElementsByTagName("option")[0].disabled = false;
document.getElementById('datalib').getElementsByTagName("option")[1].disabled = false;
document.getElementById('datalib').getElementsByTagName("option")[2].disabled = false;
document.getElementById('datalib').getElementsByTagName("option")[3].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[4].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[5].disabled = false;
document.getElementById('datalib').getElementsByTagName("option")[6].disabled = false;
document.getElementById('datalib').getElementsByTagName("option")[7].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[8].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[9].disabled = false;
document.getElementById('datalib').getElementsByTagName("option")[10].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[0].selected = true;
// Graphical Display is Redirected to Normal Display Temporarily
document.getElementById("outfmt16").disabled = true;
document.getElementById("outfmt0").disabled = false;
document.getElementById("outfmt0").checked = true;
} else {
document.getElementById('deltablast_program').style.display = "none";
}
if (program == "psiblast") {
document.getElementById('pgm_desc').innerHTML = "<a href='" + program + ".php'>⇐ Compares Protein Query vs Protein CD Database</a>";
document.getElementById('psiblast_program').style.display = "block";
document.getElementById('datalib').getElementsByTagName("option")[0].disabled = false;
document.getElementById('datalib').getElementsByTagName("option")[1].disabled = false;
document.getElementById('datalib').getElementsByTagName("option")[2].disabled = false;
document.getElementById('datalib').getElementsByTagName("option")[3].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[4].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[5].disabled = false;
document.getElementById('datalib').getElementsByTagName("option")[6].disabled = false;
document.getElementById('datalib').getElementsByTagName("option")[7].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[8].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[9].disabled = false;
document.getElementById('datalib').getElementsByTagName("option")[10].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[0].selected = true;
// Graphical Display is Redirected to Normal Display Temporarily
document.getElementById("outfmt16").disabled = true;
document.getElementById("outfmt0").disabled = false;
document.getElementById("outfmt0").checked = true;
} else {
document.getElementById('psiblast_program').style.display = "none";
}
if (program == "rpsblast") {
document.getElementById('pgm_desc').innerHTML = "<a href='" + program + ".php'>⇐ Compares Protein Query vs Protein CD Database</a>";
document.getElementById('rpsblast_program').style.display = "block";
document.getElementById('datalib').getElementsByTagName("option")[0].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[1].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[2].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[3].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[4].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[5].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[6].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[7].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[8].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[9].disabled = false;
document.getElementById('datalib').getElementsByTagName("option")[10].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[9].selected = true;
document.getElementById("outfmt16").checked = true;
document.getElementById("outfmt16").disabled = false;
} else {
document.getElementById('rpsblast_program').style.display = "none";
}
if (program == "rpstblastn") {
document.getElementById('pgm_desc').innerHTML = "<a href='" + program + ".php'>⇐ Compares Nucleotide Query vs Protein CD Database</a>";
document.getElementById('rpstblastn_program').style.display = "block";
document.getElementById('datalib').getElementsByTagName("option")[0].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[1].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[2].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[3].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[4].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[5].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[6].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[7].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[8].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[9].disabled = false;
document.getElementById('datalib').getElementsByTagName("option")[10].disabled = true;
document.getElementById('datalib').getElementsByTagName("option")[9].selected = true;
document.getElementById("outfmt16").checked = true;
document.getElementById("outfmt16").disabled = false;
} else {
document.getElementById('rpstblastn_program').style.display = "none";
}
}
function changeCSS() {
//document.getElementsByClassName('form').style.cssText = "background-color: red; color: black; font-size: 44px";
//document.getElementById('form').style.cssText = "height: 100%;";
//document.getElementById('form').style.backgroundColor = "red";
}
function enableAdvSubmit() {
document.getElementById('advsearch').disabled = false;
document.getElementById('advced').style.backgroundColor = "yellow";
document.getElementById('advced').style.color = "red";
document.getElementById('advced').style.fontWeight = "bold";
document.getElementById('advced').style.fontVariant = "small-caps";
document.getElementById('advced').style.fontFamily = "'Times New Roman', Times, serif";
}
//]]>
</script>
</head>
<body>
<?php
if(isset($_POST['search']) || isset($_POST['advsearch'])) {
if (strtoupper(substr(php_uname('s'), 0, 3)) === 'WIN') {
$osextn = ".exe";
$osstrt = "";
} else {
$osextn = "";
$osstrt = "./";
}
function convert_filter_string($filter_string, $program) {
// print STDERR "Parsing '$filter_string'\n";
if (preg_match("/F/", $filter_string, $match)) {
if (($program == "blastp" || $program == "tblastn") || ($program == "blastx" || $program == "tblastx")) {
return " -seg no";
} else {
return " -dust no";
}
}
$retval = "";
if (preg_match("/S (\d+) (\S+) (\S+)/", $filter_string, $match)) {
$retval .= " -seg '" . $match[0] . " " . $match[1] . " " . $match[2] . "'";
}
if (preg_match("/D (\d+) (\d+) (\d+)/", $filter_string, $match)) {
$retval .= " -dust '" . $match[0] . " " . $match[1] . " " . $match[2] . "'";
}
if (preg_match("/R -d (\S+)/", $filter_string, $match)) {
$retval .= " -filtering_db " . $match[0];
} elseif (preg_match("/R\s*;/", $filter_string, $match)) {
$retval .= " -filtering_db repeat/repeat_9606";
}
if (preg_match("/L|T|S|D/", $filter_string, $match) && !(preg_match("/seg|dust/", $retval, $match1))) {
if (($program == "blastp" || $program == "tblastn") || $program == "blastx") {
$retval .= " -seg yes";
} else {
$retval .= " -dust yes";
}
}
if (preg_match("/m/", $filter_string, $match)) {
$retval .= " -soft_masking true";
}
// print STDERR "returning '$retval'\n";
return $retval;
//$filter_string = "m";
//$program = "blastn";
//print convert_filter_string($filter_string, $program);
}
function blastn() {
$advparam = "";
$advparam .= " -num_alignments " . $_POST['bn_num_alignments'];
$advparam .= " -evalue " . $_POST['bn_evalue'];
$advparam .= " -word_size " . $_POST['bn_word_size'];
$match_scores = $_POST['bn_match_scores'];
$match_score = explode(',', $match_scores);
$advparam .= " -reward " . $match_score[0];
$advparam .= " -penalty " . $match_score[1];
$gapcosts = $_POST['bn_gapcosts'];
$gapcost = explode(',', $gapcosts);
$advparam .= " -gapopen " . $gapcost[0];
$advparam .= " -gapextend " . $gapcost[1];
if (isset($_POST['bn_filter1'])) {
$advparam .= convert_filter_string($_POST['bn_filter1'], $_POST['program']);
}
if (isset($_POST['bn_filter2'])) {
$advparam .= convert_filter_string($_POST['bn_filter2'], $_POST['program']);
}
return $advparam;
}
function blastp() {
$advparam = "";
$advparam .= " -num_alignments " . $_POST['bp_num_alignments'];
$advparam .= " -evalue " . $_POST['bp_evalue'];
$advparam .= " -word_size " . $_POST['bp_word_size'];
$advparam .= " -matrix " . $_POST['bp_matrix'];
$gapcosts = $_POST['bp_gapcosts'];
$gapcost = explode(',', $gapcosts);
$advparam .= " -gapopen " . $gapcost[0];
$advparam .= " -gapextend " . $gapcost[1];
if (isset($_POST['bp_filter1'])) {
$advparam .= convert_filter_string($_POST['bp_filter1'], $_POST['program']);
}
if (isset($_POST['bp_filter2'])) {
$advparam .= convert_filter_string($_POST['bp_filter2'], $_POST['program']);
}
return $advparam;
}
function blastx() {
$advparam = "";
$advparam .= " -num_alignments " . $_POST['bx_num_alignments'];
$advparam .= " -evalue " . $_POST['bx_evalue'];
$advparam .= " -word_size " . $_POST['bx_word_size'];
$advparam .= " -matrix " . $_POST['bx_matrix'];
$gapcosts = $_POST['bx_gapcosts'];
$gapcost = explode(',', $gapcosts);
$advparam .= " -gapopen " . $gapcost[0];
$advparam .= " -gapextend " . $gapcost[1];
if (isset($_POST['bx_filter1'])) {
$advparam .= convert_filter_string($_POST['bx_filter1'], $_POST['program']);
}
if (isset($_POST['bx_filter2'])) {
$advparam .= convert_filter_string($_POST['bx_filter2'], $_POST['program']);
}
return $advparam;
}
function tblastn() {
$advparam = "";
$advparam .= " -num_alignments " . $_POST['tbn_num_alignments'];
$advparam .= " -evalue " . $_POST['tbn_evalue'];
$advparam .= " -word_size " . $_POST['tbn_word_size'];
$advparam .= " -matrix " . $_POST['tbn_matrix'];
$gapcosts = $_POST['tbn_gapcosts'];
$gapcost = explode(',', $gapcosts);
$advparam .= " -gapopen " . $gapcost[0];
$advparam .= " -gapextend " . $gapcost[1];
if (isset($_POST['tbn_filter1'])) {
$advparam .= convert_filter_string($_POST['tbn_filter1'], $_POST['program']);
}
if (isset($_POST['tbn_filter2'])) {
$advparam .= convert_filter_string($_POST['tbn_filter2'], $_POST['program']);
}
return $advparam;
}
function tblastx() {
$advparam = "";
$advparam .= " -num_alignments " . $_POST['tbx_num_alignments'];
$advparam .= " -evalue " . $_POST['tbx_evalue'];
$advparam .= " -word_size " . $_POST['tbx_word_size'];
$advparam .= " -matrix " . $_POST['tbx_matrix'];
$advparam .= " -strand " . $_POST['tbx_strand'];
if (isset($_POST['tbx_filter2'])) {
$advparam .= convert_filter_string($_POST['tbx_filter2'], $_POST['program']);
}
if (isset($_POST['tbx_lcase_masking'])) {
$advparam .= " -lcase_masking";
}
return $advparam;
}
function deltablast() {
$advparam = "";
$advparam .= " -num_alignments " . $_POST['db_num_alignments'];
$advparam .= " -evalue " . $_POST['db_evalue'];
$advparam .= " -word_size " . $_POST['db_word_size'];
$advparam .= " -matrix " . $_POST['db_matrix'];
$gapcosts = $_POST['db_gapcosts'];
$gapcost = explode(',', $gapcosts);
$advparam .= " -gapopen " . $gapcost[0];
$advparam .= " -gapextend " . $gapcost[1];
$advparam .= " -threshold " . $_POST['db_threshold'];
$advparam .= " -pseudocount " . $_POST['db_pseudocount'];
return $advparam;
}
function psiblast() {
$advparam = "";
$advparam .= " -num_alignments " . $_POST['psib_num_alignments'];
$advparam .= " -evalue " . $_POST['psib_evalue'];
$advparam .= " -word_size " . $_POST['psib_word_size'];
$advparam .= " -matrix " . $_POST['psib_matrix'];
$gapcosts = $_POST['psib_gapcosts'];
$gapcost = explode(',', $gapcosts);
$advparam .= " -gapopen " . $gapcost[0];
$advparam .= " -gapextend " . $gapcost[1];
$advparam .= " -threshold " . $_POST['psib_threshold'];
$advparam .= " -pseudocount " . $_POST['psib_pseudocount'];
return $advparam;
}
function rpsblast() {
$advparam = "";
$advparam .= " -num_alignments " . $_POST['rpsb_num_alignments'];
$advparam .= " -num_descriptions " . $_POST['rpsb_num_descriptions'];
$advparam .= " -evalue " . $_POST['rpsb_evalue'];
if (isset($_POST['rpsb_filter1'])) {
$advparam .= convert_filter_string($_POST['rpsb_filter1'], $_POST['program']);
}
if (isset($_POST['rpsb_filter2'])) {
$advparam .= convert_filter_string($_POST['rpsb_filter2'], $_POST['program']);
}
if (isset($_POST['rpsb_lcase_masking'])) {
$advparam .= " -lcase_masking";
}
return $advparam;
}
function rpstblastn() {
$advparam = "";
$advparam .= " -num_alignments " . $_POST['rpstbn_num_alignments'];
$advparam .= " -num_descriptions " . $_POST['rpstbn_num_descriptions'];
$advparam .= " -evalue " . $_POST['rpstbn_evalue'];
if (isset($_POST['rpstbn_filter1'])) {
$advparam .= convert_filter_string($_POST['rpstbn_filter1'], $_POST['program']);
}
if (isset($_POST['rpstbn_filter2'])) {
$advparam .= convert_filter_string($_POST['rpstbn_filter2'], $_POST['program']);
}
if (isset($_POST['rpstbn_lcase_masking'])) {
$advparam .= " -lcase_masking";
}
return $advparam;
}
if ($_POST['adv_param'] == "advanced") {
if ($_POST['program'] == "blastn") {
$advparam = blastn();
}
if ($_POST['program'] == "blastp") {
$advparam = blastp();
}
if ($_POST['program'] == "blastx") {
$advparam = blastx();
}
if ($_POST['program'] == "tblastn") {
$advparam = tblastn();
}
if ($_POST['program'] == "tblastx") {
$advparam = tblastx();
}
if ($_POST['program'] == "deltablast") {
$advparam = deltablast();
}
if ($_POST['program'] == "psiblast") {
$advparam = psiblast();
}
if ($_POST['program'] == "rpsblast") {
$advparam = rpsblast();
}
if ($_POST['program'] == "rpstblastn") {
$advparam = rpstblastn();
}
} else {
$advparam = "";
}
$online_db = array('nr -remote', 'swissprot -remote', 'pdb -remote', 'pat -remote', 'refseq_protein -remote', 'refseq_rna -remote', 'est -remote');
$offline_db = array('db/test_na', 'db/test_aa', 'db/CDD/Smart', 'db/pdtdb');
$aa_db = array('nr -remote', 'swissprot -remote', 'pdb -remote', 'pat -remote', 'refseq_protein -remote', 'db/test_aa', 'db/CDD/Smart', 'db/pdtdb');
$na_db = array('nr -remote', 'refseq_rna -remote', 'est -remote', 'db/test_na');
$blast_aa_program = array('blastp', 'deltablast', 'psiblast', 'rpsblast');
$blast_na_program = array('blastn', 'tblastx');
$blast_tra_program = array('tblastn');
$blast_trn_program = array('blastx', 'rpstblastn');
function mol_type($seq) {
$fstr = preg_replace("/[ATCGU]/i", "", $seq);
if (strlen($fstr) > 0) {
return "aa";
} else {
return "na";
}
}
function get_seq($x) {
$fck = 0;
$seq = "";
$fl = explode("\n", $x);
$sh = trim(array_shift($fl));
if($sh == null) {
$fck++;
}
$fl = array_filter($fl);
foreach($fl as $str) {
$seq .= trim($str);
}
$seq = strtoupper($seq);
$seq = preg_replace("/[^ACDEFGHIKLMNPQRSTVWY]/i", "", $seq);
global $moltype;
$moltype = mol_type($seq);
if ((count($fl) < 1) || (strlen($seq) == 0)) {
$fck++;
return $fck;
} else {
return $fck;
}
}
function fcheck($x) {
$gt = substr($x, 0, 1);
$flck = 0;
if ($gt != ">") {
$flck++;
return $flck;
} else {
$gtr = substr($x, 1);
$sqs = explode(">", $gtr);
if (count($sqs) > 1) {
foreach ($sqs as $sq) {
$flck += get_seq($sq);
}
return $flck;
} else {
$flck += get_seq($gtr);
return $flck;
}
}
}
$error = 0;
ini_set('file_uploads', 1);
ini_set('max_execution_time', 0);
$program = $_POST['program'];
$datalib = $_POST['datalib'];
$sequence = $_POST['sequence'];
$outfmt = $_POST['outfmt'];
$seqfile = $_FILES['seqfile']['name'];
$path = realpath($_FILES['seqfile']['name']);
$tpath = realpath($_FILES['seqfile']['tmp_name']);
$extn = strtolower(pathinfo($_FILES['seqfile']['name'], PATHINFO_EXTENSION));
if (($sequence == "") && (empty($seqfile))) {
//print "<div class='error'>Input Sequence or File Not Found!</div>";
require_once('header.php');
print "Input Sequence or File Not Found!";
require_once('footer.php');
$error++;
}
if (!empty($seqfile)) {
if(!in_array($extn, array('fa', 'fas', 'fsa', 'fasta', 'seq'))) {
require_once('header.php');
print "Invalid FASTA file Input!";
require_once('footer.php');
//print "<div class='error'>Invalid FASTA file input!!</div>";
$error++;
}
}
if ($error == 0) {
if (($sequence != "") && (!empty($seqfile))) {
//print "<div class='error'>Input Either Sequence or File!</div>";
require_once('header.php');
print "Input Either Sequence or File!";
require_once('footer.php');
} else if (!empty($seqfile)) {
$input = pathinfo($_FILES['seqfile']['tmp_name'], PATHINFO_FILENAME) . ".fas";
move_uploaded_file($_FILES['seqfile']['tmp_name'], $input);
if ($outfmt == 16) {
$tmpxm = pathinfo($_FILES['seqfile']['tmp_name'], PATHINFO_FILENAME) . ".xml";
$cmd = $osstrt . $program . $osextn . " -db " . $datalib . " -query " . $input . " -outfmt " . $outfmt . " -out " . $tmpxm . $advparam;
$topfs = $tmpxm;
} else {
$tmpof = pathinfo($_FILES['seqfile']['tmp_name'], PATHINFO_FILENAME) . ".htm";
$cmd = $osstrt . $program . $osextn . " -db " . $datalib . " -query " . $input . " -outfmt " . $outfmt . " -out " . $tmpof . " -html" . $advparam;
$topfs = $tmpof;
}
$fh = fopen($input, 'r');
$f = fread($fh, filesize($input));
fclose($fh);
$status = fcheck($f);
$param_error = 0;
if ($status == 0) {
if ((in_array($program, $blast_aa_program) && in_array($datalib, $aa_db)) && ($moltype == "aa")) {
$param_error = 0;
} elseif ((in_array($program, $blast_na_program) && in_array($datalib, $na_db)) && ($moltype == "na")) {
$param_error = 0;
} elseif ((in_array($program, $blast_tra_program) && in_array($datalib, $na_db)) && ($moltype == "aa")) {
$param_error = 0;
} elseif ((in_array($program, $blast_trn_program) && in_array($datalib, $aa_db)) && ($moltype == "na")) {
$param_error = 0;
} else {
//print "<div class='error'>Invalid Input/Program/Database Selection!</div>";
require_once('header.php');
print "Invalid Input/Program/Database Selection!";
require_once('footer.php');
$param_error++;
if (file_exists($input)) { unlink ($input); }
}
if ($param_error == 0) {
print "<div id=\"progress\">";
require_once('header.php');
print "<div class='ball'></div><div class='ball'></div><div class='ball'></div><div class='ball'></div>";
require_once('footer.php');
print "</div>";
exec($cmd, $exec_output, $exec_return);
if (!$exec_return) {
$foh = fopen($topfs, 'r');
if (filesize($topfs) == 0) {
require_once('header.php');
print "Program Execution Failed!";
require_once('footer.php');
//print "<div class='error'>Program Execution Failed!</div>";
fclose($foh);
if (file_exists($input)) { unlink ($input); }
if ($outfmt == 16) {
if (file_exists($tmpxm)) { unlink ($tmpxm); }
} else {
if (file_exists($tmpof)) { unlink ($tmpof); }
}
} else {
$fo = fread($foh, filesize($topfs));
if ($outfmt == 16) {
print "<script type=\"text/javascript\">document.getElementById('progress').style.display = \"none\";</script>";
print "<div class='xoutput'><h2 style=\"text-align: center;\"><i style=\"font-size: medium\">loc</i><span style=\"color:blue; font-size: large\">BLAST</span> - <span style=\"font-size: large;\">local NCBI BLAST</span></h2><hr class='heffect' />";
print "<a href=\"index.php\" title=\"Go Back to Home\"><div style=\"padding: 0 5px 0 0;\" id=\"back\"></div></a>";
require_once('xml.php');
print "</div>";
} else {
print "<script type=\"text/javascript\">document.getElementById('progress').style.display = \"none\";</script>";
print "<div class='output'><h2 style=\"text-align: center;\"><i style=\"font-size: medium\">loc</i><span style=\"color:blue; font-size: large\">BLAST</span> - <span style=\"font-size: large;\">local NCBI BLAST</span></h2><hr class='heffect' /><div class='space' style='font-family: monospace, 'Courier New', courier;'><a href=\"index.php\" title=\"Go Back to Home\"><div style=\"padding: 0 5px 0 0;\" id=\"back\"></div></a>" . $fo . "</div></div>";
}
fclose($foh);
if (file_exists($input)) { unlink ($input); }
if ($outfmt == 16) {
if (file_exists($tmpxm)) { unlink ($tmpxm); }
} else {
if (file_exists($tmpof)) { unlink ($tmpof); }
}
}
} else {
//print "<div class='error'>Invalid Input/Program/Database Selection!</div>";
print "<script type=\"text/javascript\">document.getElementById('progress').style.display = \"none\";</script>";
include('header.php');
print "Invalid Input/Program/Database Selection!";
include('footer.php');
if (file_exists($input)) { unlink ($input); }
if ($outfmt == 16) {
if (file_exists($tmpxm)) { unlink ($tmpxm); }
} else {
if (file_exists($tmpof)) { unlink ($tmpof); }
}
}
}
} else {
require_once('header.php');
print "Invalid FASTA File Input!";
require_once('footer.php');
//print "<div class='error'>Invalid FASTA File Input!</div>";
if (file_exists($input)) { unlink ($input); }
}
} else {
$tmpif = 'blast' . date("Y.m.d.h.i.s") . '.fas';
if ($outfmt == 16) {
$tmpxm = 'blast' . date("Y.m.d.h.i.s") . '.xml';
$cmds = $osstrt . $program . $osextn . " -db " . $datalib . " -query " . $tmpif . " -outfmt " . $outfmt . " -out " . $tmpxm . $advparam;
$topfs = $tmpxm;
} else {
$tmpof = 'blast' . date("Y.m.d.h.i.s") . '.htm';
$cmds = $osstrt . $program . $osextn . " -db " . $datalib . " -query " . $tmpif . " -outfmt " . $outfmt . " -out " . $tmpof . " -html" . $advparam;
$topfs = $tmpof;
}
$fhsq = fopen($tmpif, 'w') or die("<div class='error'>File Creation Failed!</div>");
fwrite($fhsq, $sequence);
fclose($fhsq);
$sttus = fcheck($sequence);
$param_error = 0;
if ($sttus == 0) {
if ((in_array($program, $blast_aa_program) && in_array($datalib, $aa_db)) && ($moltype == "aa")) {
$param_error = 0;
} elseif ((in_array($program, $blast_na_program) && in_array($datalib, $na_db)) && ($moltype == "na")) {
$param_error = 0;
} elseif ((in_array($program, $blast_tra_program) && in_array($datalib, $na_db)) && ($moltype == "aa")) {
$param_error = 0;
} elseif ((in_array($program, $blast_trn_program) && in_array($datalib, $aa_db)) && ($moltype == "na")) {
$param_error = 0;
} else {
//print "<div class='error'>Invalid Input/Program/Database Selection!</div>";
require_once('header.php');
print "Invalid Input/Program/Database Selection!";
require_once('footer.php');
$param_error++;
if (file_exists($tmpif)) { unlink ($tmpif); }
}
if ($param_error == 0) {
print "<div id=\"progress\">";
require_once('header.php');
print "<div class='ball'></div><div class='ball'></div><div class='ball'></div><div class='ball'></div>";
require_once('footer.php');
print "</div>";
exec($cmds, $exec_output, $exec_return);
if (!$exec_return) {
$fsoh = fopen($topfs, 'r');
if (filesize($topfs) == 0) {
//print "<div class='error'>Failed to Execute!</div>";
require_once('header.php');
print "Failed to Execute!";
require_once('footer.php');
fclose($fsoh);
if (file_exists($tmpif)) { unlink ($tmpif); }
if ($outfmt == 16) {
if (file_exists($tmpxm)) { unlink ($tmpxm); }
} else {
if (file_exists($tmpof)) { unlink ($tmpof); }
}
} else {
$fot = fread($fsoh, filesize($topfs));
if ($outfmt == 16) {
print "<script type=\"text/javascript\">document.getElementById('progress').style.display = \"none\";</script>";
print "<div class='xoutput'><h2 style=\"text-align: center;\"><i style=\"font-size: medium\">loc</i><span style=\"color:blue; font-size: large\">BLAST</span> - <span style=\"font-size: large;\">local NCBI BLAST</span></h2><hr class='heffect' />";
print "<a href=\"index.php\" title=\"Go Back to Home\"><div style=\"padding: 0 5px 0 0;\" id=\"back\"></div></a>";
require_once('xml.php');
print "</div>";
} else {
print "<script type=\"text/javascript\">document.getElementById('progress').style.display = \"none\";</script>";
print "<div class='output'><h2 style=\"text-align: center;\"><i style=\"font-size: medium\">loc</i><span style=\"color:blue; font-size: large\">BLAST</span> - <span style=\"font-size: large;\">local NCBI BLAST</span></h2><hr class='heffect' /><div class='space' style='font-family: monospace, 'Courier New', courier;'><a href=\"index.php\" title=\"Go Back to Home\"><div style=\"padding: 0 5px 0 0;\" id=\"back\"></div></a>" . $fot . "</div></div>";
}
fclose($fsoh);
if (file_exists($tmpif)) { unlink ($tmpif); }
if ($outfmt == 16) {
if (file_exists($tmpxm)) { unlink ($tmpxm); }
} else {
if (file_exists($tmpof)) { unlink ($tmpof); }
}
}
} else {
print "<script type=\"text/javascript\">document.getElementById('progress').style.display = \"none\";</script>";
include('header.php');
print "Invalid Input/Program/Database Selection!";
include('footer.php');
//print "<div class='error'>Invalid Input/Program/Database Selection!</div>";
if (file_exists($tmpif)) { unlink ($tmpif); }
if ($outfmt == 16) {
if (file_exists($tmpxm)) { unlink ($tmpxm); }
} else {
if (file_exists($tmpof)) { unlink ($tmpof); }
}
}
}
} else {
//print "<div class='error'>Invalid FASTA File Input!</div>";
require_once('header.php');
print "Invalid FASTA File Input!";
require_once('footer.php');
if (file_exists($tmpif)) { unlink ($tmpif); }
}
}
}
} else {
require_once('header.php');
print "Choose Program to Use and Database to Search";
require_once('footer.php');
}
?>
</body>
</html>