g:Profiler link

#!/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 () { 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 "g:Profiler link\n", 'click here to send list of identifiers to g:Profiler', "\n", '', "\n"; close FH or die "Couldn't close $out, $!\n"; #also do link that prints text that could be pulled back into Galaxy? exit;