[Biopython-dev] [Biopython - Bug #3353] (New) Bio.KEGG.Enzymes change

[redmine at redmine.open-bio.org]

Issue #3353 has been reported by Thomas van Gurp.

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Bug #3353: Bio.KEGG.Enzymes change
https://redmine.open-bio.org/issues/3353

Author: Thomas van Gurp
Status: New
Priority: Normal
Assignee: 
Category: 
Target version: 
URL: 


When retrieving an enzyme from [[http://soap.genome.jp/KEGG.wsdl]] using 
ec_handle = client.service.bget(ec)
and Bio.KEGG.Enzyme.parse(ec_handle.split('\n'))

there is an error in the way pathways are parsed. The layout changed from:
PATHWAY     PATH: MAP00130  Ubiquinone biosynthesis

to

PATHWAY ec00030 Pentose phosphate pathway
                ec00480 Glutathione metabolism

A minor modification in the code fixes this issue:
elif keyword=="PATHWAY     ":
             if data[:5]=='PATH':
                path, map, name = data.split(None,2)
                path = 'PATH:'
                pathway = (path[:-1], map, name)
                record.pathway.append(pathway)
             else:
                map, name = data.split(None,1)
                path = 'PATH:'
                pathway = (path[:-1], map, name)
                record.pathway.append(pathway)


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