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comparison Tools/Motif_search/rules_galaxy.pl @ 0:229d36377838 draft

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author amadeo
date Mon, 05 Sep 2016 05:53:08 -0400
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-1:000000000000 0:229d36377838
1 #!/usr/bin/perl -w
2
3 $|=1;
4 use warnings;
5 use strict;
6 #Script that looks for genes that have motifs from a certain rule.
7
8 #Declaration of variables
9 my $line;
10 my $line2;
11 my @cols;
12 my @cols2;
13 my %hash;
14 my %hash1;
15 my %hash3;
16
17 my $gene;
18 my $TF;
19 my $num_motifs;
20 my @genes_rules;
21
22
23 $num_motifs=$ARGV[2];
24
25
26 open(FIMO, "<$ARGV[0]") ||
27 die "File '$ARGV[0]' not found\n";
28
29 open(OUTPUT, ">$ARGV[1]") ||
30 die "File '>$ARGV[1]' not found\n";
31
32
33 while (<FIMO>) {
34 $line=$_;
35 chomp $line;
36 @cols=split;
37 if (not $line=~/^ /){
38 $TF= substr $cols[8],5,8;
39 $gene=substr $cols[0],0,21;
40
41 if (not exists $hash{$gene}) {
42 $hash1{$gene}=0;
43
44 }
45 if (not exists $hash{$gene}{$TF}) {
46 $hash1{$gene}++;
47 $hash{$gene}{$TF}=1;
48 #print $hash1{$gene};
49 }
50
51
52 if ($hash1{$gene}==$num_motifs and not exists $hash3{$gene}) {
53 $hash3{$gene}=1;
54 #print $line, "\n";
55
56 }
57
58
59
60 }
61
62 }
63
64 close FIMO;
65 open(FIMO, "<$ARGV[0]") ||
66 die "File '$ARGV[0]' not found\n";
67
68 while (<FIMO>) {
69 $line2=$_;
70 chomp $line2;
71 @cols2=split;
72
73 if (not $line2=~/^ /){
74 $TF= substr $cols2[8],5,8;
75 $gene=substr $cols2[0],0,21;
76 foreach my $gene_listed (keys %hash3){
77
78 if ($gene_listed eq $gene) {
79 printf OUTPUT "%s\n", $line2;
80
81 }
82
83
84 }
85
86 }
87 }
88
89
90 print "Genes that have this rule:", "\n";
91 foreach my $gene_listed (keys %hash3){
92 print $gene_listed,"\n";
93 }
94
95