#!/usr/bin/perl
use warnings;
use strict;
open(FH,"file1.txt")or die "can not open file";
open(FH1,"file2.txt")or die "can not open file";
open(OUT,">result.out")or die "can not create file";

my @file1;
while(my $line1=<FH>){
my @list1=split("\t",$line1);
push(@file1,$list1[1]."#".$list1[2],$list1[4]);
}
my %hash1=@file1;

my @file2;
while(my $line2=<FH1>){
my @list2=split("\t",$line2);
push(@file2,$list2[0]."#".$list2[1],$list2[2]);
}
my %hash2=@file2;

my @allhits;
while(my ($key1,$value1)=each(%hash1)){
while(my ($key2,$value2)=each(%hash2)){
	if($key1 eq $key2){
		$value2=~s/\s//g;
		my @val1=split("/",$value1);
		my @val2=split(">",$value2);
		foreach(@val1){
			if($_ eq $val2[1]){
				print "$key1\n"
				#push(@allhits,$key1);
			}
		}
	}
}
}
=pod
foreach(@allhits){
	while(my $str=<FH1>){
		my($chrom,$position,$var,$one,$two,$three,$four,$five,$six)=split("\t",$str);
		my($id,$location)=split("#",$_);
		if(($chrom == $id) && ($position==$location)){
			print "$_";
		}
	}
}