/
transcript.cgi
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/
transcript.cgi
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#!/usr/bin/perl
use barleyrtd_wrapper;
use eorna;
use CGI;
use GD;
use strict;
my $cgi_query = CGI->new();
my $seq_name = $cgi_query->param("seq_name");
my $dataset = $cgi_query->param("dataset");
my $image_dir = "/var/www/html/barleyrtd-new/blast_net_images";
print "Content-type: text/html\n\n";
my $db_query = barleyrtd_wrapper->new('barleyrtd_new');
my($gene_name, $number) = split(/\./, $seq_name,2);
my ($contig_id) = $db_query->{'dbh'}->
selectrow_array("select contig_id from transcript_sequences where transcript_id = '$seq_name' and dataset_name=\'$dataset\'");
if ($contig_id eq ""){
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 class='img-fluid' src='images/eorna-logo.png' width=150'><span class='app-title'>EoRNA</span></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 active' 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'>
<div class='data-header'>Error Message</div>
<br>
<div class='data-body'>\n
<span class='error'>There are no transcripts in the database with ID \"$seq_name\". <br>Please enter a valid sequence identifier for the search.</span><br><br>
<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>
</main>
</div>
</div>
</body>
</html>";
die("eorna/transcript.cgi: Can't find contig source for $seq_name, $dataset\n");
}
my ($transcript_start, $transcript_stop, $chromosome) = $db_query->{'dbh'}->
selectrow_array("select min(f_start), max(f_stop), contig_id from transcript_structure where transcript_id = '$seq_name' and dataset_name=\'$dataset\' group by contig_id");
my ($nuc_seq_length, $nuc_seq) = $db_query->{'dbh'}->
selectrow_array("SELECT seq_length, seq_sequence FROM transcript_sequences WHERE transcript_id= '$seq_name' and dataset_name=\'$dataset\'");
my $protein_seq_link;
if ($seq_name =~ /BART/) {
$protein_seq_link = "<li class='nav-item'><a class='nav-link text-dark' href='#protseq'>Protein Sequence</a></li>"
}
eorna::printHeader($seq_name);
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'>
<li class='nav-item nav-link' id='nav-title'><img class='img-fluid' src='images/eorna-logo.png' width=150'><span class='app-title'>EoRNA</span></li>
<li class='nav-item nav-link' id='nav-header'><b>Gene ID</b></li>
<li class='nav-item' id='nav-info'>$gene_name <a class='nav-link' href='gene.cgi?seq_name=$gene_name&dataset=$dataset'> ➜ View Gene</a></li>
<li class='nav-item nav-link' id='nav-header'><b>Transcript ID</b></li>
<li class='nav-item' id='nav-info'>$seq_name</li>
<li class='nav-item nav-link' id='nav-header'><b>Location</b></li>
<li class='nav-item' id='nav-info'>$chromosome: $transcript_start - $transcript_stop</li>
<li class='nav-item nav-link' id='nav-header'><b>Data</b></li>
<div class='list-group ' id='list-data'>
<li class='nav-item'><a class='nav-link text-dark' href='#alt_cds'>CDS Structure</a></li>
<li class='nav-item'><a class='nav-link text-dark' href='#loc_cds'>Exon Locations</a></li>
<li class='nav-item'><a class='nav-link text-dark' href='#seq'>Nucleotide Sequence</a></li>
$protein_seq_link
</div>
<li class='nav-item nav-link' id='nav-header'><b>Utilities Menu</b></li>
<div class='list-group'>
<li class='nav-item'><a class='nav-link' href='index.html'>Home</a></li>
<li class='nav-item'><a class='nav-link' href='blast.html'>Homology Search</a></li>
<li class='nav-item'><a class='nav-link' href='keyword.html'>Annotation Search</a></li>
<li class='nav-item'><a class='nav-link' href='download.html'>Bulk Data Download</a></li>
<li class='nav-item'><a class='nav-link' href='bart_lookup.html'>Translate HORVU to BART IDs</a></li>
<li class='nav-item'><a class='nav-link' href='go.html'>GO Enrichment</a></li>
</div>
</ul>
</div>
</nav>\n\n
<main role='main' class='col-md-9 ml-sm-auto col-lg-10 pt-3 px-4'>\n";
############## Draw the transcript on the contig ###########################################
eorna::drawTranscriptsGbrowse($seq_name, $dataset, "n");
eorna::printTranscriptStructureTable($seq_name, $dataset);
############### Print out the transcript sequence ##########################################
eorna::printSequence($seq_name, "CDS", $nuc_seq, $dataset);
############### Print out the protein sequence ##########################################
if ($seq_name =~ /BART/) {
eorna::printProteinSequence($seq_name, $dataset);
}
eorna::printFooter();