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search_ids.cgi
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#!/usr/bin/perl
use eorna;
use barleyrtd_wrapper;
use CGI;
use strict;
my $cgi_query = CGI->new();
my $seq_name = $cgi_query->param("seq_name");
print "Content-type: text/html\n\n";
my $query = barleyrtd_wrapper->new('efish_genomics');
if (($seq_name =~ /^XM/) || ($seq_name =~ /^BART/)){
my $redirect;
if($seq_name =~ /XM/) {
if($seq_name =~ /\./){
$redirect = "transcript.cgi?seq_name=$seq_name&dataset=BBRACH_0.4_ncbi";
} else {
$redirect = "gene.cgi?seq_name=$seq_name&dataset=150831_barley_pseudomolecules";
}
}
if($seq_name =~ /^BART/) {
$seq_name =~ s/p/u/;
if($seq_name =~ /\./){
$redirect = "transcript.cgi?seq_name=$seq_name&dataset=150831_barley_pseudomolecules";
} else {
$redirect = "gene.cgi?seq_name=$seq_name&dataset=150831_barley_pseudomolecules";
}
}
print "<html>
<head>
<meta http-equiv=\"Refresh\" content=\"0;url=$redirect\" />
</head>
<body>
</body>
</html>";
} else {
eorna::printHeader("Error");
print "<div class='container-fluid'>
<div class='row'>
<nav class='col-md-2 d-none d-md-block grey sidebar'>
<div class='sidebar-sticky'>
<ul class='nav flex-column'>
<li class='nav-item nav-link' id='nav-title'><img src='images/eorna-logo.svg' width='150'></li>
<li class='nav-item nav-link' id='nav-header'><b>Utilities Menu</b></li>
<div class='list-group'>
<li class='nav-item'><a class='nav-link' href='index.html'>Home</a></li>
<li class='nav-item'><a class='nav-link' href='blast.html'>Homology Search</a></li>
<li class='nav-item'><a class='nav-link' href='keyword.html'>Annotation Search</a></li>
<li class='nav-item'><a class='nav-link' href='download.html'>Bulk Data Download</a></li>
<li class='nav-item'><a class='nav-link' href='bart_lookup.html'>Translate HORVU to BART IDs</a></li>
<li class='nav-item'><a class='nav-link' href='go.html'>GO Enrichment</a></li>
</div>
</ul>
</div>
</nav>
<main role='main' class='col-md-9 ml-sm-auto col-lg-10 pt-3 px-4'>\n\n";
print "<div class='data-header'>Error Message</div>
<br>
<div class='data-body'>
<span class='error'>The search term \"$seq_name\" does not match any sequence ID in the database. <br>Please enter a valid sequence identifier for the search.</span>
<div class='card-deck m-3'>
<div class='card border-dark'>
<div class='card-header option-header'>Search for a Sequence by ID</div>
<div class='card-body'>
<p><b>Barley RTD</b> : The predicted genes have the nomenclature 'BART1_0-u00001'. Transcript models are named after the the gene loci like 'BART1_0-u00001.001'.
<p><b>Morex 2017 Pseudomolecules Annotation</b> : The predicted genes have the nomenclature 'HORVU1Hr1G000010'. Transcript models are named after the the gene loci like 'HORVU1Hr1G000010.1'.
<table class='table-bordered' width='100%'><theader><tr><th>Dataset</th><th>Transcript IDs</th><th># Genes</th><th> # Transcripts</th></tr></theader>
<tbody>
<tr><td>Barley RTD</td><td>BART1_0-u00001.001</td><td>60,444</td><td>177,240</td></tr>
<tr><td>HORVU 2017</td><td>HORVU1Hr1G000010.1</td><td>81,683</td><td>334,126</td></tr>
</tbody>
</table>
<br>
<p>Searching for a gene ID will return all the transcript models from that gene region. You can go directly to a gene or transcript by using this search box:</p>
<form action='search_ids.cgi' method='get'>
<div class='input-group mb-3'>
<div class='input-group-prepend'>
<span class='input-group-text'>Search for Sequence ID</span>
</div>
<input type='text' class='form-control' name='seq_name' value='BART1_0-u00001' onfocus=\"this.value=''\">
<div class='input-group-append'><input class='btn btn-success' type='submit' value='Search'></div>
</div>
</form>
</div>
</div>
</div>
</div>\n";
eorna::printFooter();
}