[Biopython-dev] Interpro parser

[Brad Chapman]

Hi Yair;

> I found some code to work with the online version of Interpro in biopython.
> However, I couldn't find any code to parse the results. I run Interpro
> locally and am able to produce xml output. Did anyone make a parser for such
> an output?

I don't believe so. From what I've seen of InterPro in Biopython,
Kate wrote some code in Bio/WWW/InterPro.py to retrieve entries and then
some code in Bio/InterPro to deal with parsing the web output into a
Record object. I've never used the code myself but have not seen
Kate around in a while so you might feel free to take a look at it
and see if any of the objects (perhaps the InterPro Record object)
are useful to you.

> I attach an example of the Interpro output. Its clear this should be easy to
> parse, but I am not sure what would be best in that case.

The best thing to do would be to fire up a straight XML parser
included in the Python distribution (I've found the SAX parser to
work just fine) and parse it into a standard Record object.

We'd be very happy to have a full treatment of InterPro in Biopython
so if you want to have a go at this, feel free. Perhaps Kate will
chime in if she has an interest in extending her code to include XML
output and local interpro.

Thanks for looking at this!
Brad