Mercurial > repos > xuebing > sharplabtool

comparison tools/human_genome_variation/linkToGProfile.pl @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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1 #!/usr/bin/env perl
2
3 use strict;
4 use warnings;
5
6 ###################################################
7 # linkToGProfile.pl
8 # Generates a link to gprofile for a list of gene IDs.
9 # g:Profiler a web-based toolset for functional profiling of gene lists from large-scale experiments (2007) NAR 35 W193-W200
10 ###################################################
11
12 if (!@ARGV or scalar @ARGV != 4) {
13 print "usage: linkToGProfile.pl infile.tab 1basedCol idType outfile\n";
14 exit 1;
15 }
16
17 my $in = shift @ARGV;
18 my $col = shift @ARGV;
19 my $type = shift @ARGV;
20 my $out = shift @ARGV;
21
22 if ($col < 1) {
23 print "ERROR the column number should be 1 based counting\n";
24 exit 1;
25 }
26 my @gene;
27 open(FH, $in) or die "Couldn't open $in, $!\n";
28 while (<FH>) {
29 chomp;
30 my @f = split(/\t/);
31 if (scalar @f < $col) {
32 print "ERROR there is no column $col in $in\n";
33 exit 1;
34 }
35 if ($f[$col-1]) { push(@gene, $f[$col-1]); }
36 }
37 close FH or die "Couldn't close $in, $!\n";
38
39 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';
40 $link =~ s/TYPE/$type/;
41 my $g = join("+", @gene);
42 $link =~ s/GENELIST/$g/;
43 #print output
44 if (length $link > 2048) {
45 print "ERROR too many genes to fit in URL, please select a smaller set\n";
46 exit;
47 }
48 open(FH, ">", $out) or die "Couldn't open $out, $!\n";
49 print FH "<html><head><title>g:Profiler link</title></head><body>\n",
50 '<A TARGET=_BLANK HREF="', $link, '">click here to send list of identifiers to g:Profiler</A>', "\n",
51 '</body></html>', "\n";
52 close FH or die "Couldn't close $out, $!\n";
53
54 #also do link that prints text that could be pulled back into Galaxy?
55 exit;