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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 $line;
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10 my $line2;
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11 my @cols;
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12 my @cols2;
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13 my %hash;
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14 my %hash1;
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15 my %hash3;
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16
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17 my $gene;
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18 my $TF;
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19 my $num_motifs;
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20 my @genes_rules;
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21
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22
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23 $num_motifs=$ARGV[2];
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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
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29 open(OUTPUT, ">$ARGV[1]") ||
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30 die "File '>$ARGV[1]' not found\n";
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31
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32
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33 while (<FIMO>) {
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34 $line=$_;
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35 chomp $line;
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36 @cols=split;
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37 if (not $line=~/^ /){
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38 $TF= substr $cols[8],5,8;
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39 $gene=substr $cols[0],0,21;
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40
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41 if (not exists $hash{$gene}) {
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42 $hash1{$gene}=0;
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43
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44 }
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45 if (not exists $hash{$gene}{$TF}) {
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46 $hash1{$gene}++;
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47 $hash{$gene}{$TF}=1;
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48 #print $hash1{$gene};
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49 }
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50
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51
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52 if ($hash1{$gene}==$num_motifs and not exists $hash3{$gene}) {
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53 $hash3{$gene}=1;
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54 #print $line, "\n";
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55
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56 }
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57
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58
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59
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60 }
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61
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62 }
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63
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64 close FIMO;
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65 open(FIMO, "<$ARGV[0]") ||
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66 die "File '$ARGV[0]' not found\n";
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67
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68 while (<FIMO>) {
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69 $line2=$_;
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70 chomp $line2;
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71 @cols2=split;
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72
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73 if (not $line2=~/^ /){
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74 $TF= substr $cols2[8],5,8;
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75 $gene=substr $cols2[0],0,21;
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76 foreach my $gene_listed (keys %hash3){
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77
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78 if ($gene_listed eq $gene) {
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79 printf OUTPUT "%s\n", $line2;
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80
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81 }
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82
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83
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84 }
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85
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86 }
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87 }
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88
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89
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90 print "Genes that have this rule:", "\n";
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91 foreach my $gene_listed (keys %hash3){
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92 print $gene_listed,"\n";
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93 }
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94
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95
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