[Biopython-dev] Bio.MarkovModel

[Michiel de Hoon]

Hi everybody,

When I was looking at the NumPy-dependent modules, I got the impression that Bio.MarkovModel can be simplified now that it's using the new NumPy. As far as I can tell, there is no documentation for Bio.MarkovModel, and the code seems to have some (trivial) bugs that (I think) would be noticed if anybody is actively using Bio.MarkovModel. So I am wondering

1) Has anybody looked at Bio.MarkovModel in detail?
2) If not, should this module be kept?

On the one hand, Markov models are a core part of computational biology and as such are an appropriate module for Biopython. On the other hand, the code is useful only if people are actually using it. Another option is to have MarkovModel.py as a stand-alone example script of Python in computational biology instead of a full-blown module.

--Michiel.