[Biopython-dev] KEGG enhancements

Leighton Pritchard Leighton.Pritchard at hutton.ac.uk
Sat Aug 30 16:57:54 UTC 2014


Thanks Peter,

I’m very happy for the REST interface to be introduced, in place of the scraping code.

Cheers,

L.

On 30 Aug 2014, at 02:23, Peter Cock <p.j.a.cock at googlemail.com<mailto:p.j.a.cock at googlemail.com>> wrote:

On Tue, Feb 5, 2013 at 9:36 PM, Peter Cock <p.j.a.cock at googlemail.com<mailto:p.j.a.cock at googlemail.com>> wrote:
On Tue, Feb 5, 2013 at 12:33 PM, Peter Cock <p.j.a.cock at googlemail.com<mailto:p.j.a.cock at googlemail.com>> wrote:
On Tue, Feb 5, 2013 at 12:32 PM, Peter Cock <p.j.a.cock at googlemail.com<mailto:p.j.a.cock at googlemail.com>> wrote:
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,

Sorry, the correct URL, https://github.com/biopython/biopython/pull/155

Details below,

See also Leighton's blog posts about this work (with pictures):
http://armchairbiology.blogspot.co.uk/2013/01/keggwatch-part-i.html
http://armchairbiology.blogspot.co.uk/2013/02/keggwatch-part-ii.html
http://armchairbiology.blogspot.co.uk/2013/02/keggwatch-part-iii.html

Regards,

Peter

Hi all,

Given no comments positive or negative here or the original or
updated pull request (which I have just updated for Python 3),
I am inclined to apply this now (rebasing it onto the master):

https://github.com/biopython/biopython/pull/173

Once that is done, I'd like to integrate Kevin's KEGG REST API
work replacing Leighton's KGML_scrape.py code:

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

Peter


--
Dr Leighton Pritchard
Information and Computing Sciences Group; Weeds, Pests and Diseases Theme
DG31, James Hutton Institute (Dundee)
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