[Biopython-dev] KEGG support

[Kyle]

I think external library dependancies should be avoided unless necessary.
 Would a tool like wsdl2py produce code that isn't dependent on an installed
library? Alternatively, suds is LGPL based, could we just cannibalize the
source code for the important classes?

Kyle


On Wed, Feb 10, 2010 at 10:30 AM, Renato Alves <rjalves at igc.gulbenkian.pt>wrote:

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> Hi everyone,
>
> KEGG support in Biopython has been mostly untouched for the past 8 years
> with only a few changes and test additions. There is code in the tree to
> work with the Enzyme and Compound databases but not for others such as
> GENES, ORTHOLOGY, DRUG, ...
>
> Considering the fact that I will need to write some code to work with
> other formats I was planning to contribute and integrate it with the
> SeqIO interface. This will require some additional homework on my part.
>
> KEGG also has a SOAP based API [1]. It's functionality could be in some
> aspects compared to NCBI eutils. Using the python SOAP library suds [2]
> I had no problem interacting with it.
>
> So just in case someone was already working on this secretly :) I would
> like to know to make my life easier. If not I would also like to know if
> you would be interested in the addition and finally what's your thought
> about the SOAP interface and the suds (optional) dependency.
>
> Just a word on suds. Even though the project has been around for a few
> years now, it's still not available in most Linux distros. On my
> personal experience with it it's probably the simplest and easy to use
> SOAP library for python out there.
>
> Cheers,
> Renato
>
> [1] - http://www.genome.jp/kegg/soap/doc/keggapi_manual.html
> [2] - https://fedorahosted.org/suds/
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