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

[Zheng Ruan]

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.

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
)

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 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


On Mon, Apr 21, 2014 at 6:41 AM, Peter Cock <notifications at github.com>wrote:

> Congratulations all - could you also add something to the NEWS file, email
> the main list to announce this, and update the wiki as needed?
>
> —
> Reply to this email directly or view it on GitHub<https://github.com/biopython/biopython/pull/259#issuecomment-40928271>
> .
>