Hello Monks, I am back again with another problem. This script is executing fine without any error. The output file which it create with ".asc.output.cmp" are empty except one file which is 6.asc.output (@basex) containing accurate result. I feel somewhere I am doing wrong which is causing this. This script is written to compare the query file with all the other files in the directory to check for any nearby values with some threshold value entered by the user. I am very sorry for bothering you all.

#!/usr/bin/perl
# This is a script which compares the query file and base with some th
+reshold given by the user

#use warnings;
use strict;

print "Enter the Threshold Value:  \n";
my $j= <STDIN>;

my $filename1 = "10.asc.output";
my (%hash, @queryx, @queryy);

open (FILE1, $filename1) or die "can't open $filename1: $!\n";

        while(<FILE1>)
{
        if ($_ =~ /(\S+)\s+(\S+)/)
 {
        $hash{$1} = $2;
        push(@queryx,$1);
        push (@queryy, $2);
}
        }

close(FILE1);

my ($filename, $i, @basex, @basey, $folder, $a1, $a2, $a3, $b1, $b2, $
+b3, $r1, $r2, $r3, $rr1, $rr1, $rr2, $rr3);
 
$folder = '/home/users/dachs/perl_scripts/perlup'; #folder path where 
opendir(MYDIR, $folder) || die "System cant open directory reading for
+\n";


while ($filename = readdir MYDIR){
    next unless $filename =~ /\.asc.output$/i; #Check for the file .as
+c
    #undef %hash;
    #undef @basex;
    #undef @basey;
    
    open FILE, "$filename" or die "can't open $filename: $!\n"; 
    while(<FILE>){
       if ($_ =~ /(\S+)\s+(\S+)/) {
        $hash{$1} = $2;
        push(@basex,$1);
        push (@basey, $2);
          }
    }

        close (FILE);

    
open(FILEHANDLE, ">$filename.cmp") or die "cannot open file for readin
+g: $!";#Creates an output file


while ($i <= $#basex)
{
$a1 = $queryx[$i];
$a2 = $queryx[$i+1];
$a3 = $queryx[$i+2];
$b1 = $basex[$i];
$b2 = $basex[$i+1];
$b3 = $basex[$i+2];

$rr1 = (($a1) - ($b1));
$rr2 = (($a2) - ($b2));
$rr3 = (($a3) - ($b3));

$r1 = abs($rr1);
$r2 = abs($rr2);
$r3 = abs($rr3);

$i++;
print $rr1, "\n";

if (($r1 <= $j) && ($r2 <= $j) && ($r3 <= $j))
            {
        print FILEHANDLE "Matched: ", $a1, "\t", $a2, "\t", $a3, "\n";
        #$count = $count + 1;
print $r1, $r2, $r3, "\n";
            }

}
close (FILEHANDLE);
}
closedir(MYDIR);
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