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comparison Tools/Motif_search/motif_search_galaxy.pl @ 3:b30ba2b06326 draft

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author amadeo
date Mon, 05 Sep 2016 06:01:48 -0400
parents 229d36377838
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2:607d7bdfb07f 3:b30ba2b06326
1 #!/usr/bin/perl -w
2 $|=1;
3 use warnings;
4 use strict;
5
6 #Script that returns the lines of a gff file according to the ID motifs that we want.
7
8
9
10 my $motif=" ";
11 my @motifs;
12 my $line;
13 my @cols;
14 my $motif_fimo;
15
16 if ($ARGV[3] ne "#"){
17 push @motifs, $ARGV[3];
18 }
19 if ($ARGV[4] ne "#"){
20 push @motifs, $ARGV[3];
21 }
22 if ($ARGV[5] ne "#"){
23 push @motifs, $ARGV[3];
24 }
25 if ($ARGV[6] ne "#"){
26 push @motifs, $ARGV[3];
27 }
28
29
30
31
32
33 open(FIMO, "<$ARGV[0]") ||
34 die "File '$ARGV[0]' not found\n";
35 open(OUTPUT, ">$ARGV[1]") ||
36 die "File '>$ARGV[1]' not found\n";
37
38 while (<FIMO>) {
39 foreach my $tf (@motifs){
40 $line= $_;
41 chomp $line;
42 @cols=split;
43 if ($line=~/^#/){
44 printf OUTPUT "%s\n", " ";
45 }
46 elsif ($line!~/^##/ and $tf eq (substr $cols[8],5,8)) {
47
48 printf OUTPUT "%s\n", $line;
49
50
51
52 }
53 }
54
55
56 }