[Biopython-dev] KEGG API Wrapper

[Michiel de Hoon]

Hi Kevin,

It would be great to have better KEGG support in Biopython, so I think that this is useful and could in principle be merged into Biopython. But before we do so, is there some documentation for your code (or even better, for the Bio.KEGG module as a whole)? Then it's easier to see how this module can be used, and to discuss any modifications.

Thanks for your contribution!
-Michiel.

--- On Wed, 10/10/12, Kevin Wu <kjwu at ucsd.edu> wrote:

> From: Kevin Wu <kjwu at ucsd.edu>
> Subject: [Biopython-dev] KEGG API Wrapper
> To: Biopython-dev at lists.open-bio.org
> Date: Wednesday, October 10, 2012, 5:27 PM
> Hi,
> 
> I've written a simple wrapper on top of KEGG's new REST API
> (
> http://www.kegg.jp/kegg/docs/keggapi.html). The main
> functionality of this
> module is that can detect some invalid queries based on
> kegg's defined
> rules. I've implemented each of the examples given on the
> api docs as tests
> as well. Here's a quick example of its usage.
> 
> The api call to http://rest.kegg.jp/get/hsa:10458+ece:Z5100/aaseq can
> be
> done using the wrapper as:
> KEGG.query("get", ["hsa:10458", "ece:Z5100"], "aaseq")
> 
> Querying the api works well with the current parsers written
> for KEGG
> formats. Let me know if there are issues or if it's useful
> enough to be
> merged into Biopython!
> 
> https://github.com/kevinwuhoo/biopython
> 
> Thanks!
> Kevin
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