[Biopython-dev] Bio.SeqIO

[Peter]

Michiel Jan Laurens de Hoon wrote:
> 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.

Done.  I have also updated the wiki:

http://www.biopython.org/wiki/SeqIO

>> 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.

I was thinking tonight, after updating CVS, that perhaps we should try 
and find some shorter (lower case) names for "SequencesToDict" and 
"SequencesToAlignment"... something like "toDict" and "toAlignment", or 
"as_dict" and "as_alignment" might looks nicer.  e.g.

from Bio import SeqIO
my_dict = SeqIO.toDict(SeqIO.parse(handle, format))

rather than this, which looks clumsy and inconsistent:

from Bio import SeqIO
my_dict = SeqIO.SequencesToDict(SeqIO.parse(handle, format))

>> 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 have started looking over the other existing sequence parsers in 
BioPython with a view to adding some of them into the SeqIO framework 
(after the Bronx 1.43 release):

http://www.biopython.org/wiki/SeqIO_dev

Note to self (or anyone bored), I should actually write something about 
the SeqRecord class:

http://www.biopython.org/wiki/SeqRecord

>> 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.

True - but I will be away for a bit (end of March, early April) so I 
wouldn't like encourage too many people, and then not be here to help 
them.  Maybe I should try and draft something for the release notes, 
along the lines of "Beta software - please try it and give us feedback".

Peter