[BioPython] can biopython query KEGG directly?

[Giovanni Marco Dall'Olio]

On Tue, Mar 10, 2009 at 7:08 PM, Peter <biopython at maubp.freeserve.co.uk>wrote:

> On Tue, Mar 10, 2009 at 5:06 PM, Giovanni Marco Dall'Olio
> <dalloliogm at gmail.com> wrote:
> > Hi,
> > is it possible to query the KEGG database with biopython?
>
> I don't think there is any wrapper for the KEGG online API (yet).  See:
> http://www.genome.jp/kegg/soap/doc/keggapi_manual.html


well, if someone is in a hurry to query KEGG with soap, I have some scripts
(but they use the suds library).


>
>
> This does sound like a worthwhile addition (especially if the SOAP
> stuff can be done using only core python libraries included in Python
> 2.4+)


I am not sure if the SOAPpy library is the one included in the core python
libraries, and if it is since python 2.4.
For what I know, SOAPpy has ceased developed since 2005 (see
http://pywebsvcs.sourceforge.net/).
I couldn't test this library, because I still didn't managed to get it
working under an http proxy :-(.


>
>
> > .. and transform it to a SeqRecord object.
>
> We still need a Bio.KEGG gene parser, see also:
> http://bioperl.org/wiki/KEGG_sequence_format
> http://lists.open-bio.org/pipermail/biopython/2008-January/004000.html
> Once that is done, a KEGG wrapper in Bio.SeqIO would make sense.
>

I am just curious, but in which object a Kegg gene file would be transposed?
A SeqRecord? And how, exactly? I suppose all the features will go in
SeqRecord.features... but is there any standard convention to do so?
For example, the codon usage table, class, dblinks, and all the other
fields.. how they would be stored?



>
> Peter
>



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