[bip] Using motility to look for motifs

[Titus Brown]

On Sun, Dec 09, 2007 at 10:32:00PM -0800, Titus Brown wrote:
-> I've written another tutorial, "Using motility to look for motifs".
-> It's available here:
-> 
->  http://iorich.caltech.edu/~t/bio+python/motility/motility-introduction.html

There is a small bug in motility that crept into the tutorial (the 4th
'match' member of the return tuple was displayed in reverse complement
for find_exact and find_iupac); it's minor and should not have tripped
anyone up.

Nonetheless I fixed it and several other problems, and posted the
revised tutorial (now moved to the official motility docs) here:

	http://iorich.caltech.edu/~t/motility/

I found this bug because I spent a bunch of time hacking on the motility
Python interface last night, in an attempt to make it thread-happy.  You
can see a script that runs motif searches in parallel here:

	http://cartwheel.idyll.org/browser/trunk/motility/python/parallel-work-in-progress.py

although it's not very pretty ;). I only get a 50% speedup (3 seconds ->
2 seconds) on a dual-core CPU, which means there are some bottlenecks
somewhere.  Oh well.

To the good, I found an outright bug, fixed a memory leak, and revamped
the C++->Python code to become a bit more understandable.

I'll update motility to 0.8.2 sometime soon.

cheers,
--titus