[Biopython-dev] Planning for Biopython 1.54

[Andrea Pierleoni]

>
> 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.


> 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.

> As the Bio.SeqIO maintainer, I will do this,
> but right now I think getting Biopython 1.54 out should be
> prioritised. From a very quick look just now, the recent merging of
> the SFF support to the trunk will require a few tweaks in
> test_SeqIO.py (e.g. an empty file is not valid for SFF files as well
> as the UniProt XML). Also including a UniProt XML file in
> test_BioSQL_SeqIO.py would be worthwhile.
>

Mauro also added some unit testing that should be useful for this.

Let me know if you need any help/info.

Bests,

Andrea