[Biopython-dev] Bio.SeqIO

[Peter]

Michiel de Hoon wrote:
> Peter wrote:
>> SequenceIterator(handle, format)
>> SequencesToDict(sequences, key_function=None)
>> SequencesToAlignment(sequences, ...)
>> WriteSequences(sequences, handle, format)
>>
>> Does anyone want to suggest different names for these functions?

Only Michiel has replied, so I assume there are no other strong views on 
the dev mailing list.

Michiel de Hoon wrote:
> I would prefer
>>>> from Bio import SeqIO
>>>> SeqIO.read(handle, format)
>>>> SeqIO.write(sequences, handle, format)

You have persuaded me to rename SequenceIterator and WriteSequences.

BioPython uses the term "parser" all over the place.  Doing a quick 
search of the code, I found ten files with "def read(" and  fifty eight 
with "def parse(" - so I would rather have "parse" than "read".

That would give us the core functions:

Bio.SeqIO.parse(handle, format)
Bio.SeqIO.write(sequences, handle, format)

or,

Bio.SeqIO.read(handle, format)
Bio.SeqIO.write(sequences, handle, format)

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

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

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.

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

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.

Peter