Mercurial > repos > xuebing > sharplabtool

diff tools/human_genome_variation/linkToDavid.pl @ 0:9071e359b9a3
Uploaded
author: xuebing
date: Fri, 09 Mar 2012 19:37:19 -0500
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/human_genome_variation/linkToDavid.pl	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,59 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+###################################################
+# linkToDavid.pl
+# Generates a link to David for a list of gene IDs.
+###################################################
+ 
+if (!@ARGV or scalar @ARGV != 4) {
+   print "usage: linkToDavid.pl infile.tab 1basedCol idType outfile\n";
+   exit 1;
+}
+
+my $in = shift @ARGV;
+my $col = shift @ARGV;
+my $type = shift @ARGV;
+my $out = shift @ARGV;
+
+if ($col < 1) { 
+   print "ERROR the column number should be 1 based counting\n";
+   exit 1;
+}
+my @gene;
+open(FH, $in) or die "Couldn't open $in, $!\n";
+while (<FH>) {
+   chomp;
+   my @f = split(/\t/);
+   if (scalar @f < $col) {
+      print "ERROR there is no column $col in $in\n";
+      exit 1;
+   }
+   if ($f[$col-1]) { push(@gene, $f[$col-1]); }
+}
+close FH or die "Couldn't close $in, $!\n";
+
+if (scalar @gene > 400) {
+   print "ERROR David only allows 400 genes submitted via a link\n";
+   exit 1;
+}
+ 
+my $link = 'http://david.abcc.ncifcrf.gov/api.jsp?type=TYPE&ids=GENELIST&tool=summary';
+
+my $g = join(",", @gene);
+$link =~ s/GENELIST/$g/;
+$link =~ s/TYPE/$type/;
+#print output
+if (length $link > 2048) { 
+   print "ERROR too many genes to fit in URL, please select a smaller set\n";
+   exit;
+}
+open(FH, ">", $out) or die "Couldn't open $out, $!\n";
+print FH "<html><head><title>DAVID link</title></head><body>\n",
+      '<A TARGET=_BLANK HREF="', $link, '">click here to send of identifiers to DAVID</A>', "\n",
+      '</body></html>', "\n";
+close FH or die "Couldn't close $out, $!\n";
+
+exit;
author	xuebing
date	Fri, 09 Mar 2012 19:37:19 -0500
parents
children