#!/usr/bin/perl -w use strict; my @files = <*.in.sep>; my %hash; for(@files) { s/[.]in[.]sep//g } for my $file (@files) { open (my $in, "<", "$file.in.sep") || die ("cannot open $file"); open (my $out,"<", "$file.out.sep") || die ("cannot open search.txt"); %hash = map{ s/E99/99/g; $_ => $hash{$_}++;} <$in, $out>; foreach (sort keys %hash){ print "$_ $hash{$_}\n" if !$hash{$_}; } }