Mercurial > repos > amadeo > amadeo
view Tools/Second/step1_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 |
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#!/usr/bin/perl -w $|=1; use warnings; use strict; #Script that takes a gff format file from MEME suite as input and orders it by genes, #so it will create an output with all the information grouped by genes. Motifs will be mixed. #Declaration of variables my $line; my @cols; my %hash1; my %hash2; my @list1; my @list2; my $gene; my $pos1; my $n; my $index; my $position; my $scalar; my $TF; my $counter=0;#it gives you the number of lines of the gff file. It is a good way to check that the information is not lost. #Files that I am going to use if(@ARGV < 2){ print "\nUsage: step1.pl fimo.gff fimo-position-sorted.gff e\n\n"; exit(0); } #I open both files, FIMO as the input and OUTPUT as the ouput. open(FIMO, "<$ARGV[0]") || die "File '$ARGV[0]' not found\n"; open(OUTPUT, ">$ARGV[1]") || die "File '>$ARGV[1]' not found\n"; while (<FIMO>) { $line=$_; #assigning line to variable $line | $_ is a special default variable that here holds the line contents chomp $line; #avoid \n on last field @cols=split; #Splits the string EXPR into a list of strings and returns the list in list context, or the size of the list in scalar context. #This is very useful because the data of the gff file can be called using this variable. if ($line=~/^#/){ #prints the first line of the gff file that is different from the rest printf OUTPUT "%s\n", $line; $counter++; } else { #considers the other lines of the file $gene=substr $cols[0],0,21; #variable that returns the name of the gene of the line $pos1 = $cols[3]; #variable that returns the motif's start position on the gene $TF= substr $cols[8],5,8; #variable that returns the name of the motif #I use two arrays (list1 and list2) list1 returns the name of the genes and list2 the lines with all the information. #Notice that the gene and its line will have the same position in both list. if (not exists $hash1{$gene}{$TF}{$pos1}) { $hash1{$gene}{$TF}{$pos1}=1; push @list1, $gene; push @list2, $line; } } } #In this section I sort the list1 (genes) by the name of the genes, so I will take the position of every gene sorted #and I will use the position to print out the lines in the order that I want. The main function of this script #is to write the gff file but having the genes sorted by blocks. $n= scalar @list1; my @list_pos_sorted= sort { $list1[$a] cmp $list1[$b] } 0..($n - 1); for (my $i=0; $i <(scalar @list_pos_sorted); $i++){ $index=$list_pos_sorted[$i]; $position = $list1[$index]; #print $hash2{$position}; printf OUTPUT "%s\n", $list2[$index]; $counter++; } print $counter;