Basically, it seems like you are trying to get some lookup data from your first file and then use it when scanning your second file.

I would not use arrays since you mention that you have GB file sizes. I would instead use DBM::Deep which you could use to store your initial values.

A side effect is that your retrieval will be pretty quick as well.

One thing that you will need to come up with is a link between the data from the two files - some common key to use in the DBM::Deep database.

Something like this:

use strict;
use warnings;

use DBM::Deep;

my $db_filepath = 'lookup.db';
my $file1       = 'XXXX.txt';
my $file2       = 'YYYY.txt';

my $db = DBM::Deep->new($db_filepath);

open(my $fh, $file1) or die "[Error] COULD NOT OPEN FILE [$file1]-[$!]
+";

while (<$fh>) {

   my $line = $_;

   # get a common key from the data somewhere in here

   my @fields = split (/\s/ ,$line);
   my @output = grep /rs\d{5,}\b/ ,@fields;
   my $rs = join (':' , @output);
   $rs =~ s/:/\n/g;

   $db->{'some-common-key-bewtween-files'} = $rs;

}

close($fh);

# now iterate through your other file and lookup using DBM::Deep

open(my $fh2, $file2) or die "[Error] COULD NOT OPEN FILE [$file2]-[$!
+]";

while (<$fh2>) {

  my $line = $_;

  if ($line =~ /some-common-key-bewtween-files/) {

     my $db_record = $db->{'some-common-key-bewtween-files'};

     # now you have linked data from both files
     # do your other coding here.

  }

}

close($fh2);
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