[Biopython-dev] New: Uniprot XML parser

[Peter]

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