[Biopython-dev] 454 GSFlex quality score files

[Peter]

 > In Bio.Fasta there are Parsers which really belong in
 > Bio.SeqIO.FastaIO, if anywhere. How about Bio.Fasta becomes the more
 > general Fasta reader, nothing to do with sequences. ...

In actual fact, the Bio.Fasta module predates Bio.SeqIO, and I was 
thinking in a few releases time of suggesting its deprecation (but not 
just yet as for several years it was the best documented and most used 
parser in Biopython).

If we do decided keep Bio.Fasta (or extend it), then perhaps 
Bio.SeqIO.FastaIO should become just a wrapper for Bio.Fasta

I'm still digressing your ideas to turn Bio.Fasta into a generic parser 
that copes with sequences, qualities scores, or anything else.

Peter