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comparison Tools/Second/step2_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 #!/usr/bin/perl -w
2 $|=1;
3 use warnings;
4 use strict;
5
6 #Script that takes a gff format file from step1.pl as input and orders
7 #each block of gene data by the start position of the motif.
8
9 #Declaration of variables
10 my $line;
11 my @cols;
12 my %hash1;
13 my %hash2;
14 my @list1;
15 my @list2;
16 my $gene;
17 my $pos1;
18 my $n;
19 my $index;
20 my $position;
21 my $scalar;
22 my $TF;
23 my $counter=0; #it gives you the number of lines of the gff file. It is a good way to check that the information is not lost.
24
25 #Files that I am going to use
26
27 if(@ARGV < 2){
28 print "\nUsage: step2.pl fimo-gene-sorted.gff fimo-gene-&-position-sorted.gff e\n\n";
29 exit(0);
30 }
31
32 #I open both files, FIMO as the input and OUTPUT as the ouput.
33 open(FIMO, "$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 $line=$_; #assigning line to variable $line | $_ is a special default variable that here holds the line contents
40 chomp $line; #avoid \n on last field
41 @cols=split; #Splits the string EXPR into a list of strings and returns the list in list context, or the size of the list in scalar context.
42 #This is very useful because the data of the gff file can be called using this variable.
43
44 if ($line=~/^#/){ #prints the first line of the gff file that is different from the rest
45 printf OUTPUT "%s\n", $line;
46 $counter++;
47 }
48 else { #considers the other lines of the file
49 $gene=substr $cols[0],0,21; #variable that returns the name of the gene of the line
50 $pos1 = $cols[3]; #variable that returns the motif's first position on the gene
51 $TF= substr $cols[8],5,8; #variable that returns the name of the motif
52 $scalar= scalar @list1; #returns the size of the current list1
53
54 #This script stores infromation in two arrays (list1 and list2). The first one will register the first position of the motif in the
55 #gene and the list2 will store the corresponding line.
56
57 if (not exists $hash1{$gene} and not $scalar == 0) { #Every time that a new gene is considered in the loop, it will print out
58 #all the information of the previous one
59
60 #This section will print out each line of each block of genes sorted by the first position.
61 $n= scalar @list1;
62 my @list_pos_sorted= sort { $list1[$a] <=> $list1[$b] } 0..($n - 1); #This will sort the POSITION NUMBERS of the array
63 #list1 and store them in a new array name
64
65 #This will print out the information of each gene sorted by the first position. #list_pos_sorted
66 for (my $i=0; $i <(scalar @list_pos_sorted); $i++){
67 $index=$list_pos_sorted[$i];
68 #$position = $list1[$index];
69 #printf OUTPUT "%s\n",$hash2{$position};
70 printf OUTPUT "%s\n", $list2[$index];
71 $counter++;
72 }
73 }
74 if (not exists $hash1{$gene}) {#Every time that a new gene is considered in the loop, it will reset the variables
75 #so a new gene can be registered
76 %hash1=();
77 %hash2=();
78 @list1=();
79 @list2=();
80 $hash1{$gene}=1;
81 $hash2{$pos1}=$line;
82 push @list1, $pos1;
83 push @list2, $line;
84 }
85
86 elsif (exists $hash1{$gene}) { #if the next line has information of the same gene, it will
87 #store the information in the arrays.
88 $hash2{$pos1}=$line;
89 push @list1, $pos1;
90 push @list2, $line;
91 }
92
93
94 }
95
96 }
97
98 #Section that has the same structure of the previous one to print the LAST block of the file.
99 $n= scalar @list1;
100 my @list_pos_sorted= sort { $list1[$a] <=> $list1[$b] } 0..($n - 1);
101 for (my $i=0; $i <(scalar @list_pos_sorted); $i++){
102 $index=$list_pos_sorted[$i];
103 $position = $list1[$index];
104 printf OUTPUT "%s\n", $hash2{$position};
105 #printf OUTPUT "%s\n", $list2[$index];
106 $counter++;
107 }
108 print $counter;