You can open the file handle outside of the first while loop also. Because, for each iteration it will open and close the files. This will increase the system load. You can avoid this by open the file outside of the loop and move the file pointer to the starting position for each iteration.

open INDAT, "file1" or die "$!";
my @array;
my @probes;

open INCOMP, "file2" or die "$!";

while (<INDAT>){
        @array=split/\t/;
        while (<INCOMP>){
              chomp ( $_ );
                @probes=split/\t/;

                if ($array[0]=~/$probes[1]/i){
                        print $probes[1];#or whatever else 
                        }
               }
seek INCOMP, 0 , 0;
         }

         close INCOMP;
[download]

Why do you keep reopening the second file? That's probably not doing what you want. (Update: yes, that is what you want. Silly me. I should have put in the seek that vennirajan listed.)

Try the following debugging code:

Also, let's clean this up a bit (making the possibly false assumption that you want a tighter scope for the arrays since you overwrite them).

my ($file1, $file2) = qw(file1 file2);
open INDAT,  "<", $file1 or die "Cannot open ($file1) for reading: $!"
+; 
open INCOMP, "<", $file2 or die "Cannot open ($file2) for reading: $!"
+;

while (defined (my $line = <INDAT>)) {
    chomp $line; # remove newline
    my @array = split /\t/, $line;

    while (defined (my $line = <INCOMP>)) {
        chomp $line;
        my @probes = split /\t/, $line;

        # using \Q and \E to avoid having regex meta character problem
+s
        # see "perldoc perlre"
        if ($array[0] =~ /\Q$probes[1]\E/i) {
            print "Found $probes[1]\n";
        }
    }
}
close INCOMP;
close INDAT;
[download]

That should get you closer to what you're looking for. Note that we only open each file once. We also remove the newline from each line to ensure that you're not accidentally trying to match that. Also, read perlre to see how \Q and \E work (the \E is actually not necessary in the above example).

If you're using an older Perl, my three-argument open syntax won't work and you'll have to do this:

open FH, "<$file1" ...
# or
open FH, $file1 ...
[download]

Hi natoikos, Use chomp after reading a line from the files.

Try this,

open INDAT, "$file1" or die "$!";
my @array;
my @probes;
while (<INDAT>){
        chomp($_);
        @array=split/\t/;
        open INCOMP, "$file2" or die "$!";
        while (<INCOMP>){
            chomp($_);
                @probes=split/\t/;

                if ($array[0]=~/$probes[1]/i){
                        print $probes[1];#or whatever else
                        }
               }
         close INCOMP;
         }
[download]

I don't know if this would be helpful for you or not,
but after playing with your code and some example files,
I wonder if you are searching for multiple matches of $array[0] in your $probes1 list in file2,
or after finding the first match of $array[0], you want to move on to the next $array[0] and continue searching.
But I think the while loop quits running after finding the first match.
Perhaps you want to use a different loop structure.
Saints, please correct me if I am wrong.