[bip] Blog post on bioinformatics and Python

[C. Titus Brown]

On Thu, Sep 18, 2008 at 05:42:28PM +0100, Peter wrote:
-> > OTOH, frustration with the opaqueness of BioPython BLAST objects (and
-> > the use of crmpd 'sbjct' vrbl nms) led me to write my own blastparser
-> > with objecs that had a useful 'dir', were debuggable by me, had lots of
-> > automated tests, etc.  You could take a look at that, although it is
-> > sloooooooooooooooooooooow.
-> >
-> >        http://darcs.idyll.org/~t/projects/blastparser/
-> >        http://darcs.idyll.org/~t/projects/blastparser-latest.tar.gz
-> >
-> 
-> In order to maintain backwards compatibility, we are unfortunately
-> stuck with the compressed variable names now (although we could add
-> aliases).  Having a go at improving the explorablity of the BLAST
-> object structure at the python prompt is a fairly specific and
-> concrete target.  Making the __str__ and __repr__ methods here more
-> helpful is something I'd been meaning to have a go at.
-> 
-> The Biopython BLAST parsers already have plenty of tests - but I'm
-> sure there is room for more.  What license is your code under, and in
-> particular could we use any of your test files in Biopython?

You'd be more than welcome -- I spent a little while realizing that I
haven't stuck a license on it, though :).  BSD would be fine by me.

I don't know whether or not the tests will be useful, but if they are,
please take them!

--t
-- 
C. Titus Brown, ctb at msu.edu