[Bioperl-l] Fasta Qual files

[Brian A. Desany, Ph.D.]

I am just starting to get my feet wet with bioperl, so I apologize if the
answer to my question seems self-evident. (I was unable to answer this by
using the available documentation). Background: I created a tiny little
script that sorts sequences in an initial fasta file into files included.fa
and excluded.fa, based on a list of sequence ID's in a different file. That
is, for each sequence in the initial fasta file, the script goes down the
list of ID's in the index file and writes the sequence to excluded.fa if
there is a match, and if it gets to the end of the index list without
finding a match, it writes the sequence to included.fa. Then it moves on to
the next sequence in the initial fasta file and goes down the index list
again.

This works great. My question is, does bioperl have the capability of
treating fasta.qual files like this? I tried it on a fasta.qual file and it
definitely did not work! Error message about unrecognized alphabet. It
turned out that it actually did sort everything properly, but the quality
values in the output files were occasionally concatenated, such that, say,
in a run of 40 40 40 40 40 40 40, you would see 40 40 4040 40 40 40. So it
almost worked, but not quite. Is there a means to deal with fasta.qual files
within bioperl (Bio::SeqIO::fastaqual, like), or does anyone have any other
suggestions as to how to handle this independently? Thanks,
-Brian.