It would be helpful if you showed us a sample of your data (not all 5000+ lines :-) and the results you expect from it. I'm afraid I'm not quite sure what you are trying to do from your description.

A couple of points with your code.

• You try to read from your $readfile before you have opened it.
• You open your $writefile for reading, use ">" for writing.
• Your my @words = split(//,@col1); will split into individual characters, not words. You could use /\s+/ to split on whitespace to get words (depending on what your data looks like.)

I hope these initial impressions are of use to you.

Cheers,

JohnGG

Update: Two more things I just noticed.

• You seem to be trying to re-open your $wfh inside the read loop of $fh
• You read your $fh in a foreach loop. This will have the effect of reading all of the file into memory then iterating over it. Use a while loop instead which will really read the file a line at a time.

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