#!/usr/bin/perl
use strict;
use warnings;
use List::Util qw(min max); 
#max_length:最大的epitope长度
my ($outputDir,$name,$tumor_prefix,$max_length)=@ARGV;
die "usage:perl $0 outputDir name tumor_prefix max_length" if @ARGV!=4;
open IN,"$outputDir/neoantigen/MHC_Class_I/${tumor_prefix}.fasta";
my %fa;
while(<IN>){
	if (/^>MT/){
		open OUT,">$outputDir/neoantigen/MHC_Class_I/tmp.fa";
		print OUT;
		$_=~/MT\.(\d+)\./;
		my $id=$1;
		my $seq=<IN>;
		print OUT $seq;
		chomp $seq;
		$fa{$id}=$seq;	
		system"predict.py -m netchop -n $outputDir/neoantigen/MHC_Class_I/tmp.fa >>$outputDir/neoantigen/MHC_Class_I/${tumor_prefix}.cleavage.txt";
		close OUT;
	}
}
unlink "$outputDir/neoantigen/MHC_Class_I/tmp.fa";

my %score;
open IN,"$outputDir/neoantigen/MHC_Class_I/${tumor_prefix}.cleavage.txt";
while(<IN>){
	next unless /^\d+/;
	chomp;
	my @line=split;
	$line[3]=~/MT\.(\d+)\./;
	$score{$1}{$line[0]}=$line[2];
}
open IN,"$outputDir/neoantigen/MHC_Class_I/${tumor_prefix}.all_epitopes.tsv";
open OUT,">$outputDir/neoantigen/MHC_Class_I/${tumor_prefix}.all_epitopes.netchop.txt";
open OUT2,">$outputDir/neoantigen/MHC_Class_I/${tumor_prefix}.all_epitopes.netchop.filter.txt";
#my %neopt;
my $head=<IN>;
chomp $head;
print OUT "$head\tcleavage_score\n";
while(<IN>){
	chomp;
	my @line=split(/\t/);
	$line[44]=~/^(\d+)\./;
	my $id=$1;
	my $pep=$line[18];
	if(exists $fa{$id}){
		my $index=index($fa{$id},$pep)+length($pep);
		my $cleavage_score=$score{$id}{$index};
		print OUT "$_\t$cleavage_score\n";
		if ($line[21]<=5000 and ($line[23] eq "NA" or $line[23]>=1)){
			print OUT2 "$_\t$cleavage_score\n";
		}
	}else{
		print OUT "$_\tNA\n";
	}
}
system"sort -k 22 -n $outputDir/neoantigen/MHC_Class_I/${tumor_prefix}.all_epitopes.netchop.filter.txt >$outputDir/neoantigen/MHC_Class_I/${tumor_prefix}.all_epitopes.netchop.filter.sort.txt";
unlink "$outputDir/neoantigen/MHC_Class_I/${tumor_prefix}.all_epitopes.netchop.filter.txt";
open SORT,"$outputDir/neoantigen/MHC_Class_I/${tumor_prefix}.all_epitopes.netchop.filter.sort.txt";
open OUT3,">$outputDir/neoantigen/MHC_Class_I/neoantigen.txt";
print OUT3 "序号\tHLA分型\t基因\t多肽\t亲和力\t剪切效率\n";
my %pep;
my $bool=0;
while(<SORT>){
	chomp;
	my @line=split(/\t/);
	if (not exists $pep{$line[18]}){
		$pep{$line[18]}++;
		$bool+=1;
		print OUT3 "$bool\t$line[14]\t$line[11]\t$line[18]\t$line[21]\t$line[53]\n";
	}
}