Mercurial > repos > xuebing > sharplabtool
diff tools/human_genome_variation/linkToGProfile.pl @ 0:9071e359b9a3
Uploaded
| author | xuebing |
|---|---|
| date | Fri, 09 Mar 2012 19:37:19 -0500 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/human_genome_variation/linkToGProfile.pl Fri Mar 09 19:37:19 2012 -0500 @@ -0,0 +1,55 @@ +#!/usr/bin/env perl + +use strict; +use warnings; + +################################################### +# linkToGProfile.pl +# Generates a link to gprofile for a list of gene IDs. +# g:Profiler a web-based toolset for functional profiling of gene lists from large-scale experiments (2007) NAR 35 W193-W200 +################################################### + +if (!@ARGV or scalar @ARGV != 4) { + print "usage: linkToGProfile.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"; + +my $link = 'http://biit.cs.ut.ee/gprofiler/index.cgi?organism=hsapiens&query=GENELIST&r_chr=1&r_start=start&r_end=end&analytical=1&domain_size_type=annotated&term=&significant=1&sort_by_structure=1&user_thr=1.00&output=png&prefix=TYPE'; +$link =~ s/TYPE/$type/; +my $g = join("+", @gene); +$link =~ s/GENELIST/$g/; +#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>g:Profiler link</title></head><body>\n", + '<A TARGET=_BLANK HREF="', $link, '">click here to send list of identifiers to g:Profiler</A>', "\n", + '</body></html>', "\n"; +close FH or die "Couldn't close $out, $!\n"; + +#also do link that prints text that could be pulled back into Galaxy? +exit;