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1 #!/usr/bin/perl -w
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2 $|=1;
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3 use warnings;
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4 use strict;
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5
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6 #Script that takes a gff format file from MEME suite as input and orders it by genes,
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7 #so it will create an output with all the information grouped by genes. Motifs will be mixed.
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8
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9 #Declaration of variables
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10 my $line;
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11 my @cols;
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12 my %hash1;
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13 my %hash2;
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14 my @list1;
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15 my @list2;
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16 my $gene;
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17 my $pos1;
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18 my $n;
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19 my $index;
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20 my $position;
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21 my $scalar;
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22 my $TF;
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23 my $counter=0;#it gives you the number of lines of the gff file. It is a good way to check that the information is not lost.
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24
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25 #Files that I am going to use
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26
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27 if(@ARGV < 2){
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28 print "\nUsage: step1.pl fimo.gff fimo-position-sorted.gff e\n\n";
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29 exit(0);
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30 }
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31
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32 #I open both files, FIMO as the input and OUTPUT as the ouput.
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33 open(FIMO, "<$ARGV[0]") ||
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34 die "File '$ARGV[0]' not found\n";
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35 open(OUTPUT, ">$ARGV[1]") ||
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36 die "File '>$ARGV[1]' not found\n";
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37
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38
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39 while (<FIMO>) {
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40 $line=$_; #assigning line to variable $line | $_ is a special default variable that here holds the line contents
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41 chomp $line; #avoid \n on last field
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42 @cols=split; #Splits the string EXPR into a list of strings and returns the list in list context, or the size of the list in scalar context.
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43 #This is very useful because the data of the gff file can be called using this variable.
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44
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45 if ($line=~/^#/){ #prints the first line of the gff file that is different from the rest
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46 printf OUTPUT "%s\n", $line;
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47 $counter++;
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48 }
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49 else { #considers the other lines of the file
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50 $gene=substr $cols[0],0,21; #variable that returns the name of the gene of the line
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51 $pos1 = $cols[3]; #variable that returns the motif's start position on the gene
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52 $TF= substr $cols[8],5,8; #variable that returns the name of the motif
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53
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54 #I use two arrays (list1 and list2) list1 returns the name of the genes and list2 the lines with all the information.
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55 #Notice that the gene and its line will have the same position in both list.
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56 if (not exists $hash1{$gene}{$TF}{$pos1}) {
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57 $hash1{$gene}{$TF}{$pos1}=1;
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58 push @list1, $gene;
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59 push @list2, $line;
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60 }
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61
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62 }
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63
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64 }
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65
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66 #In this section I sort the list1 (genes) by the name of the genes, so I will take the position of every gene sorted
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67 #and I will use the position to print out the lines in the order that I want. The main function of this script
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68 #is to write the gff file but having the genes sorted by blocks.
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69 $n= scalar @list1;
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70 my @list_pos_sorted= sort { $list1[$a] cmp $list1[$b] } 0..($n - 1);
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71 for (my $i=0; $i <(scalar @list_pos_sorted); $i++){
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72 $index=$list_pos_sorted[$i];
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73 $position = $list1[$index];
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74 #print $hash2{$position};
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75 printf OUTPUT "%s\n", $list2[$index];
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76 $counter++;
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77 }
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78 print $counter;
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