#!/usr/bin/perl

use strict;
use threads;

my $num_of_threads = 40;

my @peptides=(); ## Store the peptides to search in array
open(IN,"peptides.txt") or die "Could not open the file:$!\n";
while(<IN>)
{
	chomp;
	$_=~s/\r//g;
	push(@peptides,$_);
}
close IN;

my %hashNR=(); ## Store the Sequence in this hash
my %hashRes=(); ## Store the matched results
my $nrid="";

open(REF,"NR.fasta") or die "Could not open the file:$!\n";
while(<REF>)
{
	chomp;
	$_=~s/\r//g;
	if(/^>/)
	{
		$nrid=(split /\s/)[0];
	}
	else
	{
		$hashNR{$nrid}.="$_";
	}
}
close REF;

my @allIDS=(keys %hashNR); 
my $L = scalar(@allIDS);
print "Reference Reading Completed\n";

my $j= 0;
while($j < scalar(@peptides))
{
	my @threads = initThreads();
	foreach(@threads)
	{
		my $pep = $peptides[$j];
		$_ = threads -> create(\&doOperation,$pep,$L);
		$j++;
	}
	foreach(@threads)
	{
		$_ -> join();
	}
}

open(OUT,">Outfile.txt") or die "Could not create the file:$!\n";
foreach my $k (keys %hashRes)
{
	print "$k\t$hashRes{$k}\n";
}
close OUT;

###############################################
## Subroutine for initializing the Thread array
sub initThreads
{
	my @initThreads;
	for(my $i=1;$i<=$num_of_threads;$i++)
	{
		push(@initThreads,$i);
	}
	return @initThreads;
}

## Task run by each threads
sub doOperation
{
	my @allp = @_;
	my $id = threads -> tid();
	for (my $i=0; $i<$allp[1]; $i++)
	{	
		if($hashNR{$allIDS[$i]}=~/$allp[0]/)
		{
			$hashRes{$allp[0]}.=",$allIDS[$i]";
		}	
	}
	threads -> exit();
}