[Biopython-dev] [biopython] Code for Codon Alignment GSoC (#259)

[Peter Cock]

On Mon, Apr 21, 2014 at 6:02 PM, Zheng Ruan <zruan1991 at gmail.com> wrote:
>
> Hi Peter and Eric,
>
> I just made some changes to my repository. The old codonalignment branch has been
> renamed to gsoc2013 for backup. I will write new code to the codonalignment branch.

OK. You could write a final GSoC blog post about this too ;)

> Eric:
> I think the whole module should be marked as experimental like the Bio.SearchIO
> module. I anticipate to enhance the codon alignment construction method as well
> as add more methods for dn/ds ratio estimation and Bayes Empirical Bayes this
> summer.
>
> I place a warning in the `__init__.py`. (https://github.com/zruan/biopython/commit/1c9e20c8a15febb7fd9219c632afb96127a006f1)

That sounds wise.

> Peter:
> The NEWS file is updated (https://github.com/zruan/biopython/commit/0dcb39bcfd48cc009edc290ceaaa3b2c2e8f806f).
> I will update the wiki shortly and make the announcement.
>
> Do I need to make a separate pull request to make the above change to biopython
> master? Or you may help me do that?

I think Eric or I can do that from those links, Eric - do you want to do this?

> I am also planning to include my latex document to Tutorial.tex. I typically use
> the Latex-Suite plugin to write latex in vim. However, it took a long time to open the
> Tutorial.tex, which made it difficult to manage. Why not put the latex code of each
> chapter into different tex file and use \include{} to import them into the main tex file?
>
> Thank you!
> Zheng Ruan

We could split the Tutorial.tex file like that - although it would mean a
bit of extra work on test_Tutorial.py (but with the benefit of getting
per-chapter line numbers).

Thank you,

Peter