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comparison Tools/Motif_search/sort_positions_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 #Script that takes a gff format file from step1.pl as input and orders
6 #each block of gene data by the start position of the motif.
7 my $line;
8 my @cols;
9 my %hash1;
10 my %hash2;
11 my @list1;
12 my @list2;
13 my $gene;
14 my $pos1;
15 my $n;
16 my $index;
17 my $position;
18 my $scalar;
19 my $TF;
20
21
22 if(@ARGV < 2){
23 print "\nUsage: step2.pl motif_search-position-sorted.gff motif_search-gene-&-position-sorted.gff e\n\n";
24 exit(0);
25 }
26
27 my $counter=0;
28 open(FIMO, "<$ARGV[0]") ||
29 die "File '$ARGV[0]' not found\n";
30 open(OUTPUT, ">$ARGV[1]") ||
31 die "File '>$ARGV[1]' not found\n";
32
33 while (<FIMO>) {
34 $line=$_;
35 chomp $line;
36 @cols=split;
37
38 if ($line=~/^ /){
39 printf OUTPUT "%s\n", $line;
40 $counter++;
41 }
42 else {
43 $gene=substr $cols[0],0,21;
44 $pos1 = $cols[3];
45 $TF= substr $cols[8],5,8;
46 $scalar= scalar @list1;
47 if (not exists $hash1{$gene} and not $scalar == 0) {
48 $n= scalar @list1;
49 my @list_pos_sorted= sort { $list1[$a] <=> $list1[$b] } 0..($n - 1);
50 for (my $i=0; $i <(scalar @list_pos_sorted); $i++){
51 $index=$list_pos_sorted[$i];
52 $position = $list1[$index];
53 #printf OUTPUT "%s\n",$hash2{$position};
54 printf OUTPUT "%s\n", $list2[$index];
55 $counter++;
56 }
57 }
58 if (not exists $hash1{$gene}) {
59 %hash1=();
60 %hash2=();
61 @list1=();
62 @list2=();
63 $hash1{$gene}=1;
64 $hash2{$pos1}=$line;
65 push @list1, $pos1;
66 push @list2, $line;
67 }
68
69 elsif (exists $hash1{$gene}) {
70 $hash2{$pos1}=$line;
71 push @list1, $pos1;
72 push @list2, $line;
73 }
74
75
76 }
77
78 }
79
80 $n= scalar @list1;
81 my @list_pos_sorted= sort { $list1[$a] <=> $list1[$b] } 0..($n - 1);
82 for (my $i=0; $i <(scalar @list_pos_sorted); $i++){
83 $index=$list_pos_sorted[$i];
84 $position = $list1[$index];
85 printf OUTPUT "%s\n", $hash2{$position};
86 #printf OUTPUT "%s\n", $list2[$index];
87 $counter++;
88 }
89 print $counter;