[BioPython] Bio.HMM

[Brad Chapman]

Hi Michiel;

> I was hoping to use the Hidden Markov Model routines in Bio.HMM in 
> Biopython. Is there any documentation or (preferably) example scripts for 
> this module available?

That code was my doing, but sadly there is really not any
documentation on it. However, the tests in the test directory might
be some guide:

test_HMMCasino.py --> Example of code usage based on a loaded dice
scenario. Basically, there are two dice, a fair and a loaded (6
comes up 1/2 of the time). The example generates rolls, and then
builds a MarkovModel and tries to predict based on the roll
frequencies which die is being used when. There are a couple of
different trainers -- BaumWelchTrainer and a KnownStateTrainer that
are used in it.

test_HMMGeneral.py --> More standard test code but at least gives an
idea of all the different functionality in the module.

The code docs are actually semi-decent, as well:

http://www.biopython.org/docs/api/public/Bio.HMM-module.html

I'd be happy for you to hack away, change, do whatever to the
module, as I haven't used it in a while myself. But definitely feel
free to ask any questions and I'll try to help as much as possible.

Brad