[Biopython-dev] New: Uniprot XML parser

[Andrea Pierleoni]

Hi Peter,
I've commented your commits directly on github, basically agreeing with
them.
Parsing PDB structures as positional features was done to capture all the
information in the uniprot file. I do not see any better place than a
SeqFeature for a positional information, the only option here is to skip it.

I saw in your repository you are using the string "uniprot-xml" to call
the parser, however the format name at the EBI REST and SOAP services
is simply "uniprotxml". take a look at:

http://www.ebi.ac.uk/Tools/webservices/services/dbfetch_rest

I think it is better to be conservative in this.

I'm still working on the SeqIO.index to make a faster implementation. RE
are really slow, and ElementTree should cope well with this task.
Anyhow it works with the current implementation, so it's not a big deal.

Andrea

> Hi Andrea,
>
> I've done some work on the plain text swiss parser to handle features,
> and some basic testing to make sure it agrees with the uniprot-xml
> parser. This showed some problems with end locations out by one
> in the XML parser which I believe I was able to resolve. I have also
> commented out the use of the skip_parsing_errors option - it doesn't
> seem to be needed and silent errors are bad.
>
> I have (for the moment) introduced a couple of new position classes
> in Bio.SeqFeature for "?123" where we have a position but it is
> uncertain, and "?" where we don't have a position at all. The later
> might be handled more elegantly by inferring a Before/AfterPosition
> instead...
>
> Note that for testing purposes, I have disabled your code where
> it builds a SeqFeature for a dbReference - I'm not sure what the
> best plan here is yet.
>
> Could you have a look at my branch please?
>
> http://github.com/peterjc/biopython/commits/uniprot
>
> Thanks,
>
> Peter
>