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1
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2 #!/usr/bin/perl
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3
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4 use strict;
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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
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10 where <args> are:
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11
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12 -i, --input <VCF input>
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13 -o, --out <output basename>
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14 ~;
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15 $usage .= "\n";
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16
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17 my ($input,$out);
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18
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19 GetOptions(
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20 "input=s" => \$input,
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21 "out=s" => \$out
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22 );
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23
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24
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25 die $usage
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26 if ( !$input);
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27
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28
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29
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30 my $nb_gene = `grep -c mRNA $input`;
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31 $nb_gene =~s/\n//g;
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32 my $nb_intergenic = `grep -c INTERGENIC $input`;
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33 $nb_intergenic =~s/\n//g;
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34
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35 my $nb_intron = `grep -c INTRON $input`;
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36 $nb_intron =~s/\n//g;
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37 my $nb_UTR = `grep -c UTR $input`;
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38 $nb_UTR =~s/\n//g;
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39 my $nb_exon = $nb_gene - $nb_intron - $nb_UTR;
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40
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41 my $nb_ns = `grep -c NON_SYNONYMOUS_CODING $input`;
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42 $nb_ns =~s/\n//g;
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43 my $nb_s = $nb_exon - $nb_ns;
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44
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45
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46
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47
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48 #system("$VCFTOOLS_EXE --vcf $input --remove-filtered-all --out $out --hardy >>vcftools.log 2>&1");
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49 system("vcftools --vcf $input --remove-filtered-all --out $out --het >>vcftools.log 2>&1");
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50 system("vcftools --vcf $input --remove-filtered-all --out $out --TsTv-summary >>vcftools.log 2>&1");
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51 system("vcftools --vcf $input --remove-filtered-all --out $out --missing-indv >>vcftools.log 2>&1");
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52
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53 open(my $G,">$out.annotation");
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54 print $G "Genic $nb_gene\n";
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55 print $G "Intergenic $nb_intergenic\n";
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56 print $G "========\n";
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57 print $G "Intron $nb_intron\n";
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58 print $G "Exon $nb_exon\n";
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59 print $G "UTR $nb_UTR\n";
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60 print $G "========\n";
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61 print $G "Non-syn $nb_ns\n";
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62 print $G "Synonym $nb_s\n";
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63 close($G);
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64
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65
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66
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67
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68
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69
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70
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