Huzzah, the crufty re-implementation of Bio::SeqIO continues unabashed by suggestions to the contrary and pointers to its documentation.

Addendum: That perhaps sounds a bit cruel, but if you don't understand enough Perl to know how to split scalars into characters you really shouldn't be trying to re-invent wheels that other people have already solved. Use the off-the-shelf widgets for the parts you can, and get fancy once you know what you're doing. Something like Beginning Perl for Bioinformatics that's aimed at biology-types specifically should help you get going.