Thanks for this it works great, however I need to run this on loads of files, I've had a play and can't seem to automate the command line arguments. Here's what I have but it doesn't work (probably because I'm not doing it right) 
#!/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.tx
+t");
    
    
    %hash = map{ s/E99/99/g; $_ => $hash{$_}++;} <$in, $out>;

    foreach (sort keys %hash){
        print "$_ $hash{$_}\n" if !$hash{$_};
    }
}

[download]
Thanks Jim

In reply to Re^2: Comparing strings from different files by Jalcock501
in thread Comparing strings from different files by Jalcock501

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