Welcome vcorby,

Your script isn't doing what you think! Please look at 'split'. You need to 'slurp' the file into an array or use a loop to get your first file. (untested)

      my @strings = ();
      open (my $F1, "<", $f1) || die "! open-100 $!";;  # open file 1 
      while ( my $input = <$F1> )
      {    chomp( $input ); # take off the line breaks
           $strings[$#strings] = $input;
      }
      close $F1;
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And life will be easier for you if you start using the 3 parameter 'open' from the beginning:

      open (my $F3, ">", $f3 ) || die "! open-300 $!";
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This gives you a start and ask more as you get closer.

Note: I like to number my 'die's so it's quicker to find the problem. If you have a 50K line script, you'll be glad you did :-).

Regards...Ed