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

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Fri Feb 20 12:58:12 EST 2009


biopython-bugzilla at maubp.freeserve.co.uk changed:

           What    |Removed                     |Added
            Summary|Entrez.efetch: dbSNP not    |Bio.Entrez.read can't parse
                   |supported yet?              |XML files from dbSNP (snp
                   |                            |database)

------- Comment #2 from biopython-bugzilla at maubp.freeserve.co.uk  2009-02-20 12:58 EST -------
I've retitled the bug to focus on the failure to parse the XML file (there is
no problem in Bio.Entrez.efetch as far as I can tell).  For example,

>>> from Bio import Entrez
>>> result = Entrez.read(Entrez.efetch(db='snp', id='9996597', retmode='xml'))
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "Bio/Entrez/__init__.py", line 286, in read
    record = handler.run(handle)
  File "Bio/Entrez/Parser.py", line 95, in run
  File "Bio/Entrez/Parser.py", line 131, in startElement
    if object!="":
UnboundLocalError: local variable 'object' referenced before assignment

This may be an NCBI bug, try this:

>>> from Bio import Entrez
>>> print Entrez.efetch(db='snp', id='9996597', retmode='xml').read()

Then copy and paste the XML into a validation site like
http://www.validome.org/xml/validate/ where I see an error.  On the other hand,
http://validator.w3.org/#validate_by_input seems happy with only a warning.

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