[Biopython-dev] [Bug 2771] New: Entrez.efetch: dbSNP not supported yet?

Fri Feb 20 11:43:20 EST 2009

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

           Summary: Entrez.efetch: dbSNP not supported yet?
           Product: Biopython
           Version: 1.49b
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: dalloliogm at gmail.com

Executing efetch on the 'snp' database returns an html file instead of an xml
(by default, running efetch on 'gene' or another database returns an xml).

>>> handle = Entrez.efetch(db='snp', id='9996597',)
>>> cont = handle.read()
>>> print cont
<html>
...
</html>

Moreover, even when forcing retmode=xml, it seems that the xml file returned is
written in an xml not supported by biopython (not sure if this a ncbi's
problem):

>>> handle = Entrez.efetch(db='snp', id='9996597', retmode='xml')
>>> cont = handle.read()
>>> print cont
'<?xml version="1.0"?>
<ExchangeSet...>
...
</ExchangeSet>

You can see the problem better if you open the result handle as explained in
the tutorial, via Entrez.read:

>>> handle = Entrez.efetch(db='snp', id='9996597', retmode='xml')
>>> result = Entrez.read(handle)
---------------------------------------------------------------------------
UnboundLocalError                         Traceback (most recent call last)

/home/gioby/Test/NCBI_wsdl/<ipython console> in <module>()

/home/gioby/usr/share/biopython/Bio/Entrez/__init__.pyc in read(handle)
    284     DTDs = os.path.join(__path__[0], "DTDs")
    285     handler = DataHandler(DTDs)
--> 286     record = handler.run(handle)
    287     return record
    288 

/home/gioby/usr/share/biopython/Bio/Entrez/Parser.py in run(self, handle)
     93         self.parser.CharacterDataHandler = self.characters
     94         self.parser.ExternalEntityRefHandler =
self.external_entity_ref_handler
---> 95         self.parser.ParseFile(handle)
     96         self.parser = None
     97         return self.object

/home/gioby/usr/share/biopython/Bio/Entrez/Parser.py in startElement(self,
name, attrs)
    129             self.attributes = attrs
    130             return
--> 131         if object!="":
    132             object.tag = name
    133             if attrs:

UnboundLocalError: local variable 'object' referenced before assignment

Try this code also, it will return a different error:
>>> handle = Entrez.efetch(db='snp', id='9996597')   # retmode is HTML
>>> result = Entrez.read(handle)

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