#!/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 () { 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 "DAVID link\n", 'click here to send of identifiers to DAVID', "\n", '', "\n"; close FH or die "Couldn't close $out, $!\n"; exit;