I have a few suggestions.

1. Rephrase your question using complete sentences, capitalization, punctuation, and maybe even paragraphs. We don't require that you use the Queen's English, but your post has to be basically intelligible, which yours isn't really right now.
2. Provide at least a rough sketch, using code in what you know of Perl, of what your program is actually going to do. Posting real code that you've already written and explaining where you're stuck is even more helpful.
3. Take a look at some documentation. system explains how to simply call an external program from Perl, and perlopentut explain ways of passing data back and forth from external programs, and also how to write or append data to text files. bioperl has a lot of resources for manipulating gene sequence data and the like with Perl.

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