use strict;
use warnings;

use Tie::File;
use Fcntl qw(O_RDONLY);

my $file1 = 'file1.txt';
my $file2 = 'file2.txt';
my $file3 = 'file3.txt';

my %result;

#-- Process file 1

tie my @file1_arr, 'Tie::File', $file1, mode => O_RDONLY;

foreach my $record ( @file1_arr) {
    my @id = $record =~ m/HWI\-(.*)\#/g; # extract ID's
    my @rez = split(/\t/, $record, 4);

    # Save some info for later
    $result{$id[0]} = [ @rez[1,2] ];     # assume is only 1 ID :)
}

untie @file1_arr; # finished with file 1

#-- Process file 2 and write output to file 3

tie my @file2_arr, 'Tie::File', $file2, mode => O_RDONLY;

#-- The result file
tie my @content, 'Tie::File', $file3;

foreach my $record ( @file2_arr) {

    my @id = $record =~ m/HWI\-(.*)\#/g;

    my $data2 = $result{$id[0]}[0]; #print " D2 $data2\n";
    my $data3 = $result{$id[0]}[1]; #print " D3 $data3\n";

    # Output
    my @rez = split(/\t/, $record, 4);
    my $record_new = "$id[0] $data2 $rez[1] " . abs($data3 - $rez[2]);
    push @content, $record_new;
}

untie @file2_arr; # finished with file 2
untie @content;   # all finished