[Biopython-dev] KEGG enhancements

[Peter Cock]

Hi all,

We have a couple of new pull requests for KEGG enhancements,
which we can look at after the imminent Biopython 1.61 release
goes out this week.

Kevin's working on the REST API,
https://github.com/biopython/biopython/pull/152

Leighton's working on KGML and graphics,
https://github.com/biopython/biopython/pull/153

There is a tiny bit of online access code in Leighton's code
which can probably be changed to use Kevin's work - I've
not had time to examine the overlap yet.

Peter


---------- Forwarded message ----------
From: kevin <notifications at github.com>
Date: Mon, Feb 4, 2013 at 8:03 PM
Subject: [biopython] Add KEGG API Querying Support (#152)
To: biopython/biopython <biopython at noreply.github.com>


This adds support to query KEGG's REST API
(http://www.kegg.jp/kegg/docs/keggapi.html) along with simple tests
which ensure that the correct url is hit and documentation in the
cookbook.

This has been discussed on the mailing list in the following thread:
http://lists.open-bio.org/pipermail/biopython-dev/2012-October/009981.html.

________________________________

You can merge this Pull Request by running

  git pull https://github.com/kevinwuhoo/biopython master

Or view, comment on, or merge it at:

  https://github.com/biopython/biopython/pull/152

Commit Summary

Added a KEGG API Wrapper
Forgot copyright
Added a general parser and a KEGG section in the tutorial.
Updated querying code and corresponding tests.
Updated documentation to reflect changes in KEGG module.

File Changes

M Bio/KEGG/__init__.py (196)
M Doc/Tutorial.tex (88)
M Tests/output/test_KEGG (41)
M Tests/test_KEGG.py (159)

Patch Links:

https://github.com/biopython/biopython/pull/152.patch
https://github.com/biopython/biopython/pull/152.diff