[Biopython-dev] GSoC Project Update -- 5

[Wibowo Arindrarto]

Hi everyone,

I just posted another update on my GSoC project here:
http://bow.web.id/blog/2012/06/hello-indexers/

A brief summary:

* I added the SearchIO indexing functions, with the same interface as
SeqIO's indexing functions. It currently supports all the available
SearchIO parsers (blast-tab, blast-xml, and hmmer-text).
* (not mentioned in the post) I did some refactoring to the SearchIO
code base. It was starting to get a bit messy, but now it's cleaner.
All the parsers are now implemented as classes. For some of them,
users can use it directly to tweak its behavior (e.g. the blast-tab
parser can be used to parse plain blast-tab files with custom column
ordering. This is not possible if users use SearchIO.parse or
SearchIO.read instead).

Additionally, I should also mention that my schedule has been changed
slightly. The original plan for next week was to focus on hmmer-text
indexing. However, since it has been done (except for the testing,
which should not take a week), I will be focusing on writing the
SearchIO converters. So expect to see that instead.

That's all for now :).

regards,
Bow