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1 #!/usr/bin/perl -w
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2
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3 $|=1;
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4 use warnings;
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5 use strict;
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6 #Script that looks for genes that have motifs from a certain rule.
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7
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8 #Declaration of variables
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9 my %hash;
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10 my $line;
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11 my @cols;
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12 my @pos;
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13 my @motif;
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14 my @genes;
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15 my $pos1;
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16 my $gene;
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17 my $TF;
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18 my $current_gene;
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19 my $size;
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20
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21 if(@ARGV < 2){
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22 print "\nUsage: testrules_galaxy.pl fimo.gff testrules.gff \n\n";
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23 exit(0);
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24 }
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25
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26 open(FIMO, ">$ARGV[0]") ||
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27 die "File '$ARGV[0]' not found\n";
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28 open(OUTPUT, "<$ARGV[1]") ||
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29 die "File '<$ARGV[0]' not found\n";
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30
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31 $current_gene="";
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32
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33 while (<FIMO>) {
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34 $line=$_;
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35 @cols=split;
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36 $TF= substr $cols[8],5,8;
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37 $gene=substr $cols[0],0,21;
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38 $pos1 = $cols[3];
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39 $size=scalar @motif;
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40 if (not exists $hash{$gene} ) {
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41
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42 if ($current_gene ne "") {
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43 printf OUTPUT "%s\n", $current_gene, " ", "=>"," ";
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44 }
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45 for (my $i=0;$i<$size;$i++){
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46 printf OUTPUT "%s\n", $motif[$i],"($pos[$i])","\t";
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47 }
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48 print "\n";
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49 @motif=();
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50 @pos=();
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51 $current_gene=$gene;
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52 push @motif,$TF;
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53 push @pos, $pos1;
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54
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55 $hash{$gene}=1;
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56
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57
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58 }
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59
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60 else {
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61 push @motif,$TF;
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62 push @pos, $pos1;
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63 }
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64
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65 }
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66
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67 $size=scalar @motif;
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68 printf OUTPUT "%s\n", $current_gene, " ", "=>"," ";
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69 for (my $i=0;$i<$size;$i++){
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70 printf OUTPUT "%s\n", $motif[$i],"($pos[$i])","\t";
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71 }
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72
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73
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