72 lines
1.7 KiB
Perl
Executable File
72 lines
1.7 KiB
Perl
Executable File
#!/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},${tumor})=@ARGV;
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open IN,"${outputDir}/mutation/hotspot/${tumor}.hotspot.snp.indel.anno.hg19_multianno.txt";
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open OUT,">${outputDir}/mutation/hotspot/${tumor}.hotspot.snp.indel.anno.hg19_multianno_filter.txt";
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open HT,"/dataseq/jmdna/codes/public/hotspot.bed";
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my %ht;
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while(<HT>){
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chomp;
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my @line=split;
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$ht{$line[3]}=1;
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}
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my $head=<IN>;
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my @ht;
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while(<IN>){
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chomp;
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my @line=split(/\t/);
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next if $line[8] eq 'synonymous SNV';
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my @hgvs=split(/,/,$line[9]);
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my $hgvs=$hgvs[0];
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if (my $transcript=&transcript($line[6])){
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if(grep{/$transcript/}@hgvs){
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$hgvs=(grep{/$transcript/}@hgvs)[0];
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}
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}
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$line[9]=$hgvs;
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$hgvs=~/(\S+):(\S+):(\S+):c\.(\S+):p\.(\S+)/;
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my($gene,$nm,$exon,$c,$p)=($1,$2,$3,$4,$5);
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my $key1=$gene."_".$p;
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my ($key2,$key3)=(1,1);
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if($p=~/del/){
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$key2=$gene."_".$exon."_del";
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}elsif($p=~/ins/){
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$key2=$gene."_".$exon."_ins";
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}elsif($p=~/^(\S\d+)\S/){
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$key3=$gene."_".$1;
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}
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if(exists $ht{$key1} or exists $ht{$key2} or exists $ht{$key3}){
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push @ht,join("\t",@line);
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}
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}
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if(@ht){
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print OUT "$head";
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print OUT join("\n",@ht);
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}
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sub transcript{
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my $gene=shift @_;
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open TR,"/dataseq/jmdna/codes/reportbase/oncokbgene.txt";
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my %oncogene;
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while(<TR>){
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chomp;
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my @line=split;
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$oncogene{$line[0]}=$line[2];
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}
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if (exists $oncogene{$gene}){
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$oncogene{$gene}=~s/\.\d+//;
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return $oncogene{$gene};
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}else{
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print "$gene has no NM id in oncokbgene.txt";
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return "";
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}
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}
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