[Biopython-dev] GSoC Project Update -- 3

[Wibowo Arindrarto]

Hi everyone,

I just posted my latest GSoC update here:
http://bow.web.id/blog/2012/05/from-bio-import-searchio/

To summarize the post and what I've done the last week:

* I finished writing all base SearchIO objects and tested them as
well. These objects are the QueryResult object (previously called
Result), representing search results from a single query; the Hit
object, representing pairwise alignments from a single database hit;
and the HSP object, representing a single alignment. I've also written
the docstrings for these objects, so you can run help() on them in an
interpreter session. The post also includes a very brief outline of
the base objects' features, if you are curious.

* Using this, I was able to write a working prototype for SearchIO
BLAST XML parsing. This prototype has also been tested, using the test
cases I've generated previously. For now, it's implemented using our
NCBIXML parser, just so that people can have a taste of what SearchIO
will feel like. If you want to play around with the prototype, it's
available here:
https://github.com/bow/biopython/tree/searchio-blastxml.

As always, feel free to notify me of suggestions, critiques, and/or
feature requests :).

regards,
Bow