People have raised several issues in your code already, I will not repeat them, but will add some more that may be of help. You are much better off using Bioperl to read fasta files. You will be able to do much more and easily with bioperl. And as another gentle piece of advice is to learn ( say from this site or the Bioperl site ) on how to format your code so it doesnt look like its being pressed against a wall. People like to see lean code... but not lean in the way you have here...
"with perl on my side"
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