47 lines
945 B
Perl
47 lines
945 B
Perl
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#!/usr/bin/env perl
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use strict;
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use warnings;
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die "usage:perl $0 tumor normal output" unless @ARGV == 3;
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my ($tumor, $normal, $output) = @ARGV;
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open T, "$tumor";
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open N, "$normal";
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open OUT, "> $output";
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my %n;
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while (<N>) {
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next if /^#/;
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chomp;
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my @line = split;
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my $freq = (split(":", $line[-1]))[4];
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my $key = join '_', @line[0, 1, 3, 4];
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$n{$key} = $freq;
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}
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while (<T>) {
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if (/^#/) {
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print OUT;
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next;
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}
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chomp;
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my @line = split;
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my $freq = (split(":", $line[-1]))[4];
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my $key = join '_', @line[0, 1, 3, 4];
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if (not exists $n{$key}) {
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print OUT "$_\n";
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next;
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}
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else {
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# 去除对照样本中频率大于0.05的
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if ($n{$key} >= 0.05) {
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next;
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}
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else {
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# 频率是对照样本的五倍？
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if ($freq / $n{$key} > 5) {
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print OUT "$_\n";
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}
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}
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}
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}
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