[Biopython-dev] 454 GSFlex quality score files

[Jared Flatow]

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