[Biopython-dev] [Bug 2771] Bio.Entrez.read can't parse XML files from dbSNP (snp database)

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2771





------- Comment #4 from dalloliogm at gmail.com  2009-02-24 07:04 EST -------
(In reply to comment #3)
> (In reply to comment #2)
> > This may be an NCBI bug, ...
> 
> According to this page there is/was a problem with the XML files returned for
> the snp database by efetch,
> http://eutils.ncbi.nlm.nih.gov/entrez/query/static/esoap_help.html
> 
> >> Known issues
> >> * ...
> >> * eFetch utility generates an invalid XML for SNP, so currently it doesn't
> >>   work through SOAP. The bug is being fixed.
> >> * ...
> 
> Unfortunately I have no idea if that information is current or not.  This could
> been unrelated.

Yeah, unfortunately the XML seems to be still invalid.
I have tried to paste an XML result from Bio.Entrez to many XML validators, but
they detect errors.
I have also tried with a python module to interrogate SOAP services (suds) and
it also return errors.
> 


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