[Biopython] biopython parse for KEGG gene file

[Peter Cock]

Hi Nafiz,

If you look at Leighton's example, you'll see the KEGG REST API
and KGML parsing code is now in Biopython. This was included in
Biopython 1.65 onwards (contributions from Kevin Wu, Leighton,
and a little from me).

If you have a KEGG subscription and want to work on and contribute
parsers for other files beyond enzymes and compounds, that would
be useful too.

Thanks,

Peter

On Wed, May 18, 2016 at 9:06 AM, Leighton Pritchard
<Leighton.Pritchard at hutton.ac.uk> wrote:
> Hi Nafiz,
>
> My understanding is that you are correct, with respect to parsing files from
> the local filesystem (I may be wrong though…).
>
> There is an alternative way to get access to KEGG data through the online
> REST API, and there’s a summary/set of worked examples for this interface
> here:
> https://github.com/widdowquinn/notebooks/blob/master/Biopython_KGML_intro.ipynb
> that I hope you might find useful. Since KEGG adopted a subscription model,
> I’ve used this interface for all my KEGG work.
>
> Best wishes,
>
> L.
>
> On 17 May 2016, at 20:04, Md Nafiz Hamid <nafiz.hamid.iut at gmail.com> wrote:
>
> Hi,
>
> Is there a biopython parser for KEGG gene files. I was only able to find
> parsers for enzyme and compound files.
>
> Thanks,
> Nafiz