I almost can't believe no one's suggested this to you, but have you looked at Beginning Perl for Bioinformatics? From the description: "This book shows biologists with little or no programming experience how to use Perl..."

Seems to me like a good place to start for you, but I must add the disclaimer that I am not a biologist, and I've never picked up this book myself. It might be worth checking out though.

Also, I stand by the folks that talk about emacs (especially with cperl mode installed) and the command line perl interpreter as being the way to go. use strict; and use warnings;, get the feel of the perl debugger, and make ample use of the chatterbox and SOPW, and I'm sure you'll be fine.