Hi,

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.

Try this,

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]

Regards,
S.Venni Rajan.
"A Flair For Excellence."
                -- BK Systems.