hi monks, i have 2 files. i have to compare the contents of specific columns between the two files, and print the results. it sounds simple, but am getting into trouble when i code. the files looks like this(each file is 500MB in size).the number of lines in both the files are not equal:

sample file1:
ast578    61218    15755    +    C/A
ast579    61218    15856    -    A/G/T
ast580    61218    65798    +    T/C
ast581    61218    67955    -    A/TTA/AT
ast582    61218    68625    +    -/G/AT
ast599    61218    68025    +    (AT)12/34/32

sample file2:
61218    15755    A > T    0    4    0    0    2    7
61218    15856    T > C    3    2    0    3    1    8
61218    42547    A > G    3    7    5    4    1    6
61218    67955    A > G    0    10    0    9    3    4
61218    68625    G > A    0    10    0    8    1    5
[download]

Here, the 2nd,3rd, and last columns of the file1 is compared with the 1st,2nd,and 3rd column of the file2. if the single alphabet before '>' symbol in file2 matches with the single alphabet between '/' symbol in file1, the line(file2) is reported as hit and printed in the result. its reported only if the match to file1 is a single alphabet, otherwise, no. the 1st column of file1 is appended to the hits of file2 lines and is reported as output. output file looks like this:

61218    15755    A > T    0    4    0    0    2    7    ast578
61218    15856    T > C    3    2    0    3    1    8    ast579
61218    67955    A > G    0    10    0    9    3    4    ast581
[download]

the program which i have written so far is:

#!/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)=sp
+lit("\t",$str);
        my($id,$location)=split("#",$_);
        if(($chrom == $id) && ($position==$location)){
            print "$_";
        }
    }
}
[download]

The program is taking a longggg time to run. can anyone please suggest a simpler way :( i would be really thankful if you can help on this :)

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