[Biopython] biopython parse for KEGG gene file

[Leighton Pritchard]

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<mailto: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


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
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