you've asked questions about this code before, at about regular expression. you took ryan's advice, which gets your regular expressions closer to working, but is still broken. it will fail if intron or exon have no value between quotes (eg.             /exon="").

i think you should go back and read all the responses to your query. there's some good advice in there (okay, it's from me and trs80), including code samples *with comments!* that will help you understand what you are doing. also, there's some good recommended reading... no required reading. i'll put those links here again.

some nodes you might want to read are:
while or foreach?
Opening files
Use strict warnings and diagnostics or die
Death to Dot Star!

as well as shift, FileHandle, perlre, split, and while.

please, use strict!

~Particle