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PathwayGene.pl
executable file
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PathwayGene.pl
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#!/usr/local/bin/perl
# Copyright SRA International
#
# Distributed under the OSI-approved BSD 3-Clause License.
# See http://ncip.github.com/pathway-interaction-database/LICENSE.txt for details.
use CGI;
use strict;
BEGIN {
my @path_elems = split("/", $0);
pop @path_elems;
push @INC, join("/", @path_elems);
}
if (-d "/app/oracle/product/dbhome/current") {
$ENV{'ORACLE_HOME'} = "/app/oracle/product/dbhome/current";
}
use PathwayOld;
my ($db_user, $db_pass, $db_inst, $schema) =
("web", "readonly", "cgprod", "pid");
my $query = new CGI;
my $gene = $query->param("gene");
my $genes_a = $query->param("genes_a");
my $genes_b = $query->param("genes_b");
my $format = $query->param("format");
my $pathway = $query->param("pathway");
my $what = $query->param("what");
my $source = $query->param("source");
my $file_a = $query->param("FILE_A");
my $file_b = $query->param("FILE_B");
#my ($what, $genes, $format, $pathway, $source) = ("pathway", "207", "gif", 500055, "Reactome");
#my ($what, $genes_a, $format, $pathway, $source) = ("rank", "207,2208,2885,3122,3123,3159,3497,3561,3565,3566,3716,3718,6198,6464,6778", "text");
#my ($what, $genes_a, $format, $pathway, $source) = ("rank", lc("AKT1,BRCA1,BARD1"), "text");
my $db = DBI->connect("DBI:Oracle:" . $db_inst, $db_user, $db_pass);
if (not $db or $db->err()) {
print STDERR "Cannot connect to " . $db_user . "@" . $db_inst . "\n";
exit;
}
if ($what eq "rank") {
if ($format eq "text") {
print "Content-type: text/plain\n\n";
} elsif ($format eq "html") {
print "Content-type: text/html\n\n";
} else {
print "Content-type: text/plain\n\n";
print "for what='rank', format is 'text' or 'html'\n";
exit;
}
} elsif ($what eq "pathway") {
if ($pathway !~ /^\d+$/) {
print "Content-type: text/plain\n\n";
print "for what='pathway', specify pathway=<numeric pathway id>\n";
exit;
}
if ($format eq "svg") {
print "Content-type: text/html\n\n";
} elsif ($format eq "gif") {
print "Content-type: text/html\n\n";
} else {
print "Content-type: text/plain\n\n";
print "for what='pathway', format is 'svg' or 'gif'\n";
exit;
}
if ($source eq "") {
print "Content-type: text/plain\n\n";
print "for what='pathway', specify source=<source name>\n";
exit;
}
} else {
print "Content-type: text/html\n\n";
my @lines;
push @lines, "<html>";
push @lines, HTML_HEAD();
push @lines, "</head>";
push @lines, "<body>";
push @lines, "<h3>Rank Pathways By Gene Lists</h3>";
push @lines, "<blockquote>";
my $form = new CGI;
push @lines, "<br>";
push @lines, "<p>Upload one or two lists of Entrez Gene ids:";
push @lines, "<br>";
push @lines, $form->start_multipart_form(-method=>'POST',-action=>'PathwayGene.pl');
push @lines, $form->hidden(-name=>'what',-value=>'rank');
push @lines, "<blockquote>";
push @lines, "Gene List A\ ";
push @lines, $form->filefield(-name=>'FILE_A',-size=>30);
push @lines, "<br><br>";
push @lines, "Gene List B\ ";
push @lines, $form->filefield(-name=>'FILE_B',-size=>30);
push @lines, "<br>";
push @lines, "<ul>";
push @lines, "<li>Genes only in List A will be colored blue";
push @lines, "<li>Genes only in List B will be colored red";
push @lines, "<li>Genes in both lists (and complexes with components in both lists ) will be colored purple";
push @lines, "</ul>";
push @lines, "</blockquote>";
push @lines, "Pick format:";
push @lines, "<blockquote>";
push @lines, $form->radio_group(-name=>'format', -linebreak=>'true',
-values=>['html','text'], -labels=>{'html'=>'HTML','text'=>'text'},
-default=>'html');
push @lines, "</blockquote>";
push @lines, $form->submit(-label=>'Rank Pathways');
push @lines, "<br>";
push @lines, $form->end_form;
push @lines, "<br>";
push @lines, "</blockquote>";
print join("\n", @lines, "");
exit;
}
my (%genes_a, %genes_b);
for my $g (split(",", $genes_a)) {
$genes_a{$g} = 1;
}
if ($gene ne "") {
$genes_a{$gene} = 1;
}
for my $g (split(",", $genes_b)) {
$genes_b{$g} = 1;
}
my $g;
my $error;
if ($file_a) {
while (<$file_a>) {
s/\n//g;
s/\r//g;
s/^ +//;
($g) = split /\t/;
$g = lc($g);
if ($g eq "") {
next;
}
# if ($g =~ /^\d+$/) {
$genes_a{$g} = 1;
# } else {
# $error++;
# print "File A has non-numeric (bad) Entrez Gene id: $g<br>\n";
# }
}
}
if ($file_b) {
while (<$file_b>) {
s/\n//g;
s/\r//g;
s/^ +//;
($g) = split /\t/;
$g = lc($g);
if ($g eq "") {
next;
}
# if ($g =~ /^\d+$/) {
$genes_b{$g} = 1;
# } else {
# $error++;
# print "File B has non-numeric (bad) Entrez Gene id: $g<br>\n";
# }
}
}
if ($error) {
exit;
}
if ($what eq "rank") {
if ($format eq "html") {
print HTML_HEAD();
print "<h3>Pathways Ranked by Probability of Containing Genes from Query Lists</h3>";
}
print RankPathwaysByGeneHits($db, $schema, $format, \%genes_a, \%genes_b);
} elsif ($what eq "pathway") {
my $mols_a = GetMolIdsForEntrezGene($db, $pathway, \%genes_a);
my $mols_b = GetMolIdsForEntrezGene($db, $pathway, \%genes_b);
print CreateGraphicFile($db, $schema, $pathway, $source, $mols_a, $mols_b, $format);
}
$db->disconnect();