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

[Zheng Ruan]

Hi,

I integrate my document into the Tutorial (
https://github.com/zruan/biopython/tree/codonalignment/Doc)
as chapter 18. Meanwhile, I split each chapter into the `chapter` directory
and include them to the
Tutorial.tex. The test_Tutorial.py is also updated accordingly, which is
able to report per-chapter line
numbers if the doctest fails.

Best,
Zheng



On Mon, Apr 21, 2014 at 1:06 PM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> 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
>