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9
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1 #!/usr/bin/perl
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2
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3 use strict;
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4
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5 use Getopt::Long;
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6 use Bio::SeqIO;
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7
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8 my $usage = qq~Usage:$0 <args> [<opts>]
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9 where <args> are:
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10 -v, --vcf <VCF input>
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11 -o, --out <output>
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12 -s, --step <step (in bp)>
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13 ~;
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14 $usage .= "\n";
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15
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16 my ($vcf,$out,$step,$min_depth);
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17 $min_depth = 5;
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18
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19 GetOptions(
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20 "vcf=s" => \$vcf,
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21 "out=s" => \$out,
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22 "min_depth=s"=> \$min_depth,
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23 "step=s" => \$step,
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24 );
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25
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26
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27 die $usage
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28 if ( !$vcf || !$step || !$out );
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29
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30 if ($step =~/^(\d+)\s*$/){
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31 $step = $1;
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32 }
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33 else{
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34 die "Error: step size must be an integer\n";
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35 }
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36
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37
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38 my $VCFTOOLS_EXE = "vcftools";
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39
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40 my %max;
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41 my %counts_ns;
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42 my %counts_s;
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43 my $nb_gene = 0;
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44 my $nb_intergenic = 0;
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45 my $nb_exon = 0;
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46 my $nb_intron = 0;
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47 my $nb_UTR = 0;
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48 my $nb_syn = 0;
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49 my $nb_nsyn = 0;
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50 if ($vcf =~/\.bcf/){
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51 system("$VCFTOOLS_EXE --bcf $vcf --recode --recode-INFO-all --out $out");
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52 $vcf = "$out.recode.vcf";
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53 }
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54 open(my $VCF,$vcf);
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55 while(<$VCF>)
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56 {
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57 my @infos = split(/\t/,$_);
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58 if (scalar @infos > 8 && !/#CHROM/)
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59 {
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60 my $chrom = $infos[0];
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61 my $position = $infos[1];
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62 my $id = $infos[2];
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63
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64
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65 my $classe_position = int($position/$step);
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66 if (/=NON_SYNONYMOUS_CODING/){
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67 $counts_ns{$chrom}{$classe_position}++;
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68 $nb_nsyn++;
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69 }
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70 if (/=SYNONYMOUS_CODING/){
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71 $counts_s{$chrom}{$classe_position}++;
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72 $nb_syn++;
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73 }
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74 if (/INTERGENIC/){
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75 $nb_intergenic++;
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76 }
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77 elsif (/EFF=/){
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78 $nb_gene++;
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79 }
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80 if (/CODING/){
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81 }
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82 elsif (/UTR/){
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83 $nb_UTR++;
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84 }
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85 elsif (/INTRON/){
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86 $nb_intron++;
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87 }
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88 $max{$chrom} = $classe_position;
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89 }
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90 }
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91 my $nb_exon = $nb_gene - $nb_intron - $nb_UTR;
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92
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93 open(my $OUT,">$out");
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94 #print $OUT "Chrom Bin Nb synonymous SNPs Nb non-synonymous SNPs dN/dS ratio\n";
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95 print $OUT "Chrom Bin dN/dS ratio\n";
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96 foreach my $chrom(sort keys(%counts_s))
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97 {
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98 my $maximum = $max{$chrom};
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99 for(my $i=1;$i<=$maximum;$i++)
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100 {
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101 my $classe_position = $i;
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102 my $nb_s = 0;
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103 my $nb_ns = 0;
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104 my $ratio = 0;
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105 if ($counts_s{$chrom}{$classe_position}){$nb_s = $counts_s{$chrom}{$classe_position};}
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106 if ($counts_ns{$chrom}{$classe_position}){$nb_ns = $counts_ns{$chrom}{$classe_position};}
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107 if ($nb_s){$ratio = $nb_ns/$nb_s;}
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108 my $bin = $classe_position * $step;
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109 #print $OUT "$chrom $classe_position $nb_s $nb_ns $ratio\n";
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110 print $OUT "$chrom $bin $ratio\n";
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111 }
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112 }
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113 close($OUT);
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114
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115
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116
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117 open(my $A2, ">$out.location");
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118 print $A2 "Intergenic $nb_intergenic Intergenic:$nb_intergenic\n";
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119 print $A2 "Genic $nb_gene Exon:$nb_exon Intron:$nb_intron UTR:$nb_UTR\n";
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120 close($A2);
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121
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122 open(my $A2, ">$out.effect");
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123 print $A2 "Intron $nb_intron Intron:$nb_intron\n";
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124 print $A2 "UTR $nb_UTR UTR:$nb_UTR\n";
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125 print $A2 "Exon $nb_exon Synonym:$nb_syn Non-syn:$nb_nsyn\n";
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126 close($A2);
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127
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