Regarding BioPerl, I have not used it, but you may be able to get more information by reading the Tutorial -> Perl and Bioinformatics

If you still want to pursue developing your own script, you need to provide more information:

• Post small, relevant samples of your input files, preferably less than 10 lines each.
• Post the actual output you get, including any errors or warnings.
• Post the output you want.
• use strict and warnings

The goal is to post something self-contained that anyone of us can download and run.

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