[Biopython-dev] Codon Alignment GSoC Update

[Eric Talevich]

Hi Zheng,

Nice work this week. For the next tasks:

1. It's probably not a high priority to implement all of the dN/dS
approaches described in Yang's book (i.e. LWL85m, LPB93, Ina95), beyond the
simple early methods (NG86, LWL85)  and the finale, YN00. If you get around
to doing them all, cool, but if you only have time to do one more I'd pick
YN00.

2. SciPy is a relatively large dependency, so I recommend making it a
runtime import -- do the import from within the function that needs it,
rather than at the top-level scope of the module. E.g.:
Bio.Phylo._utils.to_networkx

3. Where are you focusing your documentation efforts? If you're keeping
most of the descriptions in the docstrings, it would be convenient to
format the text as reStructuredText for processing with Epydoc and Sphinx.
Time permitting, it would also be nice to have a chapter on this work in
the Tutorial, see Doc/Tutorial.tex (also fine to write this up as a
separate LaTeX document first and roll it in later).

Cheers,
Eric


On Sun, Aug 11, 2013 at 3:04 PM, Zheng Ruan <zruan1991 at gmail.com> wrote:

> Hi all,
>
> An update of Codon Alignment Project can be found at (http://zruanweb.com/).
> In the next week, I will be implementing the Maximum Likelihood method for
> dN/dS ratio estimation. I do not anticipate to write any code for the
> optimization and Scipy's functionality is most suitable to be used here.
> This might be a new dependency for Biopython. Is it okay to add this? Or
> are there some other functions in Biopython for optimization problems?
> Thanks!
>
> Best,
> Zheng Ruan
>