[Biopython-dev] Bio.SeqIO

[Michiel Jan Laurens de Hoon]

Peter wrote:
> That would give us the core functions:
> 
> Bio.SeqIO.parse(handle, format)
> Bio.SeqIO.write(sequences, handle, format)

That sounds good to me.

> I'll let you [Michiel] make the call.  Say the word and I'll update the 
> code and the wiki today.

Just to avoid any misunderstanding: While I have been in charge of 
building the Biopython releases, unfortunately that doesn't come with 
any official decision-making power :-(.

> Are you happy with Bio.SeqIO.SequencesToDict(...) name?

Well I think that this function is not so essential as Bio.SeqIO.parse 
and Bio.SeqIO.write. So I'll let you decide.

> I think we should keep Bio.SeqIO.SequencesToAlignment(...) for the time 
> being, until we do some work on the Bio.Align class.  I don't think we 
> should tackle this before the next release.  I'm happy to document this 
> particular function as "experimental/beta" and liable to be removed or 
> replaced in future.

OK.

> After the renaming, I would say the Bio.SeqIO code is OK for release.

OK then I'll try for the Bronx-release (1.43) for sometime during next 
week. If we find some issues with the new code after this release, we 
can do another release (code-named Queens) shortly after.
I'll get started on updating the documentation for the new Bio.Blast 
parsers.

> After BioPython 1.43 is out, I would like to mark the old code in 
> Bio/SeqIO/FASTA.py and Bio/SeqIO/generic.py as depreciated.

As far as I'm concerned, you can also deprecate them before this 
release. This will encourage people to start using Bio.SeqIO, and 
improve our changes on finding any remaining problems.

Thanks for all your work on Bio.SeqIO, and for involving the Biopython 
community in its development. I think Bio.SeqIO is a major improvement 
for Biopython.

--Michiel.


-- 
Michiel de Hoon
Center for Computational Biology and Bioinformatics
Columbia University
1130 St Nicholas Avenue
New York, NY 10032