[Biopython-dev] New: Uniprot XML parser

[Andrea Pierleoni]

Hi Everyone,
I've been using a lot biopython in the last couple of years, it is very
useful to me. So now it's my turn to contribute and be helpful to someone
else.
I wrote a parser for the Uniprot XML format, that is reasonably fast (8000
entries/min on a core2duo mainstream PC). The main improvements with the
actual SwissProt flat file parser are a deeper parsing of comment fields,
and a Seqrecord containing features.

The parser is based on the ElementTree library and was successfully tested
on the complete SwissProt database (v57.12). Thus I think it is ready to
be released.

I followed the rules to develop a new parser for SeqIO, filed an
enhancement bug to bugzilla (bug 2992), and included the parser in a
public biopython fork on github available at:

http://github.com/apierleoni/biopython/tree/uniprotxml-branch

the new parser is in the "uniprotxml-branch" branch, and the parser code
is in Bio/SeqIO/UniprotIO.py

The parser can be used from SeqIO using:

iterator=SeqIO.parse(handle,'uniprot')


I think this could be easily integrated in Biopython,  unit test is still
missing, but should be very easy to do.
Anyhow any code review or suggestions are welcome.

Andrea