[Biopython-dev] Bio.MarkovModel

[Peter]

On Sun, Oct 5, 2008 at 3:07 AM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
> 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.

That's good, but of limited benefit in itself.

> As far as I can tell, there is no documentation for Bio.MarkovModel, and

There isn't even a copyright statement - but there are at least
docstrings, which is something.  Looking at the CVS log, Jeff Chang
checked this in originally, so either he wrote it or he should at
least know who did.

> 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?

Not personally.

> 2) If not, should this module be kept?

I would say yes.

> 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.

As you say, Markov models are an important tool in computational
biology, so having some useful code to work with them in Biopython is
a good thing.  To me, having this remain as a "top level" module in
Biopython would give it higher status and visibility than hiding it
away in the example scripts.

If you can see a few little things that need fixing, then making those
improvements would be worthwhile.  If you don't really have the time
to deal with them now, even just filing bugs would be worth doing.

If anyone is actively using the module, then contributing something
for the tutorial would be very welcome.  If you don't know LaTeX (used
for the typesetting), then just plain text is fine - I'm happy to deal
with the formatting.

Peter