You still haven't provided enough context free of jargon from your problem domain to let people clearly answer your question. Reading I know what I mean. Why don't you? and How (Not) To Ask A Question would probably be helpful at this point. Don't make people drag everything out of you tooth and nail in order to give you help.

Update: Not to mention given the apparent problem domain if this is a common file format it's likely BioPerl has an off the shelf module to do this already . . .