I'm sorry, I am a Biology student and I have merely had perl suggested to me as a means to an end in order to get my data into a usable format.

Right, and you're merely trying to write a perl program -- might as well learn the basics of the syntax, like what goes in a match operator is not an attempt to read from a filehandle -- you have to separate the steps

Are you sure an already written perl program, say something from the bioperl.org website wasn't suggested instead?