[Biopython-dev] Planning for Biopython 1.54

[Peter Cock]

On Thu, Mar 11, 2010 at 5:43 PM, Andrea Pierleoni
<andrea at biocomp.unibo.it> wrote:
>
>>
>> Hi Andrea,
>>
>> Your UnitProt XML parser was one of the things I thought we should
>> delay until after getting Biopython 1.54 out the door, but I would
>> expect it to be included in Biopython 1.55.
>>
>> There are at least two remaining issues, (1) where to save the comment
>> fields, and (2) what to call the format in SeqIO. Both of these should
>> ideally be run by BioPerl and EMBOSS on the openbio-l mailing list to
>> ensure the OBF projects which use simple strings for file formats are
>> consistent. Would you like me to start a discussion there regarding
>> the format name? e.g. Should it be "uniprot", "uniprot-xml", or maybe
>> even "unitprotxml". Personally, "uniprot" seems fine provided this is
>> going to be the primary file format for UniProt records in the short
>> to medium term.
>
> Of course you are free to open a discussion. I used 'uniprot' for sake of
> simplicity, but then I noticed that the format is called 'uniprotxml' in
> EBI REST web services. A common name will easier for everybody.

In that case, given the EBI REST convention, uniprotxml may be wise.

>> Also I don't think any of the current Biopython developers have sat
>> down to review the code.
>
> The code was reviewed by Mauro Amico, I don't know if he is one of the
> "current Biopython developers", anyhow any additional review is welcome.

I don't recall Mauro Amico contributing to Biopython in the past, but
as you say, the more eyes on the code the better :)

Peter