[Biopython-dev] 454 GSFlex quality score files

[Peter]

Jared Flatow wrote:
> 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.

Well I'm currently just making a suggestion for the future, deprecating 
Bio.Fasta, we should still canvas opinion on the main mailing list 
before taking that action.

>> 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.

That was a typo, but you managed to guess my meaning. I meant to say: 
I'm still digesting [i.e. thinking about] 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.

I'll take a look, Bug 2382 - Generic FASTA parser
http://bugzilla.open-bio.org/show_bug.cgi?id=2382

Peter