Thanks! the two files will always be in sync because file A is generated from a log of a code run over file B, and then parsed by a script which ensures this. One question though 
        $line{$.} = undef if /$X/;

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Should it not be $line{$.} = undef if /X/? I dont want $X because the pattern can be anywhere. when I say $line{$.} = undef does this mean that this is undefined, but "exists"?

In reply to Re^2: This has me stumped, pattern matching, 2 files by tsk1979
in thread This has me stumped, pattern matching, 2 files by tsk1979

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