[Biopython] biopython parse for KEGG gene file

[Md Nafiz Hamid]

Hi,

Thanks for the Ipython notebook, it looks like a great resource. As I
suspected though, at the moment,
there is no parser for the gene files.

I have written a minimalistic parser for my purposes but I will be glad to
make it all purpose and
contribute to biopython. I do not have a KEGG subscription so I have worked
with the KEGG REST API
in biopython. Thanks for all the clarification.

Best Regards,
Nafiz

Md Nafiz Hamid
Graduate Research Assistant
Bioinformatics and Computational Biology
Department of Veterinary Microbiology and Preventive Medicine
2178 Vet Med
Iowa State University
Ames, IA 50011-1250

On Wed, May 18, 2016 at 4:00 AM, Peter Cock <p.j.a.cock at googlemail.com>
wrote:

> 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
>
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