#!/usr/bin/perl
use strict;
use warnings;

die "usage:perl $0 outputDir tumor" if @ARGV!=2; 
my (${outputDir},${tumor})=@ARGV;

open IN,"${outputDir}/mutation/hotspot/${tumor}.hotspot.snp.indel.anno.hg19_multianno.txt";
open OUT,">${outputDir}/mutation/hotspot/${tumor}.hotspot.snp.indel.anno.hg19_multianno_filter.txt";

open HT,"/dataseq/jmdna/codes/public/hotspot.bed";
my %ht;
while(<HT>){
	chomp;
	my @line=split;
	$ht{$line[3]}=1;
}


my $head=<IN>;
my @ht;
while(<IN>){
	chomp;
	my @line=split(/\t/);
	next if $line[8] eq 'synonymous SNV';
	my @hgvs=split(/,/,$line[9]);
	my $hgvs=$hgvs[0];
	if (my $transcript=&transcript($line[6])){                                      
		if(grep{/$transcript/}@hgvs){
			$hgvs=(grep{/$transcript/}@hgvs)[0];
		}
	}
	$line[9]=$hgvs;
	$hgvs=~/(\S+):(\S+):(\S+):c\.(\S+):p\.(\S+)/;
	my($gene,$nm,$exon,$c,$p)=($1,$2,$3,$4,$5);
	my $key1=$gene."_".$p;
	my ($key2,$key3)=(1,1);
	if($p=~/del/){
		$key2=$gene."_".$exon."_del";
	}elsif($p=~/ins/){
		$key2=$gene."_".$exon."_ins";	
	}elsif($p=~/^(\S\d+)\S/){
		$key3=$gene."_".$1;
	}
	if(exists $ht{$key1} or exists $ht{$key2} or exists $ht{$key3}){
		push @ht,join("\t",@line);
	}
}

if(@ht){
	print OUT "$head";
	print OUT join("\n",@ht);
}

sub transcript{
        my $gene=shift @_;
        open TR,"/dataseq/jmdna/codes/reportbase/oncokbgene.txt";
        my %oncogene;
        while(<TR>){
                chomp;
                my @line=split;
                $oncogene{$line[0]}=$line[2];                   
        }
        if (exists $oncogene{$gene}){
                $oncogene{$gene}=~s/\.\d+//;
                return $oncogene{$gene};
        }else{
                print "$gene has no NM id in oncokbgene.txt";
                return "";
        }
}