Mercurial > repos > amadeo > amadeo
view Tools/Motif_search/motif_search_galaxy.pl @ 3:b30ba2b06326 draft
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author | amadeo |
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date | Mon, 05 Sep 2016 06:01:48 -0400 |
parents | 229d36377838 |
children |
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#!/usr/bin/perl -w $|=1; use warnings; use strict; #Script that returns the lines of a gff file according to the ID motifs that we want. my $motif=" "; my @motifs; my $line; my @cols; my $motif_fimo; if ($ARGV[3] ne "#"){ push @motifs, $ARGV[3]; } if ($ARGV[4] ne "#"){ push @motifs, $ARGV[3]; } if ($ARGV[5] ne "#"){ push @motifs, $ARGV[3]; } if ($ARGV[6] ne "#"){ push @motifs, $ARGV[3]; } open(FIMO, "<$ARGV[0]") || die "File '$ARGV[0]' not found\n"; open(OUTPUT, ">$ARGV[1]") || die "File '>$ARGV[1]' not found\n"; while (<FIMO>) { foreach my $tf (@motifs){ $line= $_; chomp $line; @cols=split; if ($line=~/^#/){ printf OUTPUT "%s\n", " "; } elsif ($line!~/^##/ and $tf eq (substr $cols[8],5,8)) { printf OUTPUT "%s\n", $line; } } }