[Biopython-dev] pypaml

Peter Cock p.j.a.cock at googlemail.com
Fri Jun 10 10:58:37 UTC 2011

On Fri, Jun 10, 2011 at 11:53 AM, Brandon Invergo <b.invergo at gmail.com> wrote:
> There is one other problem. As you may recall, I decided to
> reimplement the Chi2 program from the PAML package to provide a
> convenient means to do likelihood ratio testing without having to load
> another library (scipy, rpy2). The original was written in C but had
> limited command-line options so I couldn't just write an interface to
> it. Re-writing the code in Python seemed to work fine, as far as
> getting the correct results/output. However, I later found that doing
> tests with large degrees of freedom (one codeml model comparison
> requires 41 df) takes an exorbitant amount of time compared to the C
> code. So, I see three options: dig into the code to try to find ways
> to optimize it, look into something like Weave for compiling the C
> code into a Python module, or just remove Chi2 for now and wait for
> him to release a version that takes command line arguments (which he
> claims is coming in the next version). Any thoughts on this matter?

Adding C code has drawbacks as it has to compile on multiple
platforms, and cannot be used in Jython (and likely not in IronPython
or PyPy - I've not kept up to date with their progress). Also, it doesn't
see a good use of time to reimplement something the next version
of PAML will include.

I would wait for the next version of Chi2.


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