[Biopython-dev] Bio.Sequencing

[Cymon Cox]

2009/6/29 Peter Cock <p.j.a.cock at googlemail.com>

>  >> It would also make sense to have a writer in Bio.Sequencing.Phd
> >> taking its Record objects (and have Bio.SeqIO turn SeqRecord
> >> objects into PhD Record objects, and call that). Perhaps this would
> >> be a better idea as it is more flexible, but it would be more work,
> >> and could be slower ;)
> >
> > Yes, this was my concern. As I have it now, the parser code is in
> > Bio.Sequencing.Phd and is called by the Bio.SeqIO.PhdIO, but
> > the writer code is in PhdIO. I could move the write_record to the
> > Phd module for symmetry, but as all the Phd attributes can be
> > stored in SeqRecord, the Phd parser code could just as rationally
> > be moved to PhdIO.
>
> For now, having the writer in Bio.SeqIO.PhdIO seems fine. We
> could as a second step make the Bio.SeqIO.PhdIO parse self
> contained, and as a third step, declare Bio.Sequencing.Phd
> obsolete.


This sounds like a plan. I'll try and get it all together and push it to
github sometime today.

Cheers, C.
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