well I tested it on different files,
but the main idea is: 
foreach (<*.in.sep>){
        $name = $` if /.in.sep/;
        open IN, $_ or die $!;
        open OUT, $name.'.out.sep' or die $!;
                %hash = map{ s/E99/99/g; $_ => $hash{$_}++;} <IN>, <OU
+T>;
        close IN, OUT;

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

[download]
correct if there are mistakes,
or if it might be optimized
ty)

In reply to Re^3: Comparing strings from different files by Lennotoecom
in thread Comparing strings from different files by Jalcock501

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