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