[bip] Ensembl API

[C. Titus Brown]

On Thu, Sep 18, 2008 at 03:07:26PM +0100, Peter Saffrey wrote:
-> This post is as much to lend another voice to the crowd as anything else.
-> 
-> I've only been in Bioinformatics a few months (from straight computer 
-> science), but have already found the prevalence of Perl to be a worry. 
-> At the moment, the code I'm working with is small enough to be rewritten 
-> in Python, making it far easier for me to maintain and extend it, as 
-> well as remain sane.
-> 
-> However, as others have pointed out, there's not a great deal you can do 
-> if all the APIs you need to use are in Perl. Does anybody else work with 
-> Ensembl, retrieving and manipulating gene sequences? Are there any 
-> options for doing this in Python?
-> 
-> I know gene databases are mirrored elsewhere - do any of these places 
-> have a Python interface?

Hi, Peter,

a Google Summer of Code student, Jenny Qian, spent the summer using
pygr's SQL mapper and schema mechanisms to create a prototype
'pyensembl' interface.  You can download a prototype here,

	http://code.google.com/p/pygr/

under "Featured Downloads".

You'll have to talk to Jenny (CCed) about the exact status, but I
*think* that it's got about 1/3 of the ENSEMBL API implemented.  Now
that the summer is over the pace of work is going to slow down, but I
believe Jenny is planning to continue working on it.

Unfortunately (or fortunately?) Jenny's work also pointed out a number
of places where a "code generation" approach would be better than the
current pygr approach, and so it may be a while yet before we can
easily implement the full ENSEMBL API.

cheers,
--titus
-- 
C. Titus Brown, ctb at msu.edu