[Biopython-dev] 454 GSFlex quality score files
Jared Flatow
jflatow at northwestern.edu
Tue Oct 16 16:11:04 EDT 2007
On Oct 16, 2007, at 2:33 PM, Peter wrote:
> > 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).
>
I see, it looks like its meant to be deprecated, I was just saying
its actually doing SeqIO functionality.
> 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.
I'm not quite sure you're meaning of digressing, if you mean thinking
it over, then great =) Otherwise I hope you'll seriously consider it
anyway. Either way, I think I posted a more coherent message on
bugzilla with some example data and motivation.
jared
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