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

my ($output_dir,$tumor)=@ARGV;
die "useage:perl $0 output_dir tumor" unless @ARGV==2;

open IN,"$output_dir/mutation/${tumor}.snp.indel.Somatic.annoall.hg19_multianno.txt";
<IN>;
open OUT,">${output_dir}/mutation/${tumor}.tmb.txt";
print OUT "可信\tChr\tStart\tEnd\tRef\tAlt\tExonicFunc\tTranscript\tGene\tBasechange\tAAchange\tfreq\tTotal_reads\tMutant_reads\tStrand_bias\tCOSMICID\tdbSNP\tFilter\tTSG/OG\n";

##TSG_OG
my (%tsg,%og);
open TSG,"/dataseq/jmdna/codes/reportbase/snv_indel_mutation.csv";
<TSG>;
while(<TSG>){
	chomp;
	my @line=split(",");
	if($line[-1] eq 'Yes'){$tsg{$line[0]}=1;}
	if($line[-2] eq 'Yes'){$og{$line[0]}=1;}	
}



while(<IN>){
	chomp;
	my @line=split(/\t/,$_);
	my $freq=(split(":",$line[-2]))[-2];
	my $FREQ=$freq=~s/%//r;
	if($FREQ>=5 and $line[5]=~/exonic/ and $line[5]!~/ncRNA/ and $line[8] ne "unknown" and $line[17]<0.01 and ($line[$#line]!~/STR/ or (length($line[3])>=4 or length($line[4])>=4) or
        $FREQ>5) and $line[18]<0.01 and $line[19]<0.01 and  $line[20]<0.01 and $line[23]<0.01 and $line[28]<0.01 and $line[32]<0.01){
		my @hgvs=split(/,/,$line[9]);
		my $hgvs=$hgvs[0];
		if (my $transcript=&transcript($line[6])){					
			if(grep{/$transcript/}@hgvs){
				$hgvs=(grep{/$transcript/}@hgvs)[0];
			}
		}
		$line[9]=$hgvs;
		$hgvs=~/(NM.*):exon\d+:(c.*?):(p\..*)/;
		my($transcript,$Basechange,$protein)=($1,$2,$3);
		my $COSMICID=(split(";",$line[11]))[0];
		if ($COSMICID=~/\./){
			$COSMICID="/";
		}
		my($dp,$vd,$vfr)=(split(":",$line[-2]))[2,4,-1];
		$vfr=join(",",(split(",",$vfr))[2,3]);
		my $tsg=(exists $tsg{$line[6]} and exists $og{$line[6]})?"TSG/OG":(exists $tsg{$line[6]})?'TSG':(exists $og{$line[6]})?'OG':'.';
		my @anno=('1',@line[0,1,2,3,4,8],$transcript,$line[6],$Basechange,$protein,$freq,$dp,$vd,$vfr,$COSMICID,$line[10],$line[101],$tsg);
		print OUT join("\t",@anno),"\n";
	}
}


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 "";
	}
}