chomp($input = <STDIN>);
...
    chomp($output = <STDIN>);
...
open (INPUT, "$input") || die "died opening input\n";#opening up ngc188cata and putting it into INPUT#

open (STDOUT, ">$output") || die "died opening output\n"; #opening up ngc188cat2 and setting output of out#
##</code><code>##

  open(INPUT, "<", $input) or die ...
  open(OUTPUT, ">", $output) or die ...
or
  open(INPUT, "< $input") or die ...
  open(OUTPUT, "> $output") or die ...