41 lines
772 B
Perl
41 lines
772 B
Perl
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#!/usr/bin/perl
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#use strict;
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#use warnings;
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die "usage:perl $0 outputDir tumor" if @ARGV!=2;
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my (${outputDir},${tumor})=@ARGV;
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open L,"${outputDir}/mutation/hotspot/${tumor}.hotspot.L.snp.indel.vcf";
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open H,"${outputDir}/mutation/hotspot/${tumor}.hotspot.H.snp.indel.vcf";
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my %high;
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my %low;
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my @head;
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while(<L>){
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if(/^#/){
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push @head,$_;
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}else{
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my @line=split;
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$low{"$line[0]_$line[1]"}=$_;
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}
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}
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while(<H>){
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unless(/^#/){
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my @line=split;
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$high{"$line[0]_$line[1]"}=$_;
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}
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}
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my @content;
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foreach my $key(keys %low){
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if(not exists $high{$key}){
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push @content,$low{$key};
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}
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}
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if (@content){
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open OUT,">${outputDir}/mutation/hotspot/${tumor}.hotspot.snp.indel.vcf";
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print OUT @head;
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print OUT @content;
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}
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