[BioPython] GenBank.NCBIDictionary broken?

[Kael Fischer]

Sometime in the past few weeks GenBank.NCBIDictionary seems to have stopped 
working.  Typical traceback follows.

I don't see anything promising in the CVS heads.  This may be a problem in 
Bio.db or EUtils, I suppose.  Does anyone have more information about this.

Any ideas about where one would start digging around?


 >>> from Bio import GenBank
 >>> gb = GenBank.NCBIDictionary('nucleotide','fasta')
 >>> gb['28201044']
Traceback (most recent call last):
   File "<stdin>", line 1, in ?
   File 
"/usr/local/src/py_bioinformatics/biopython-1.30/build/lib.linux-i686-2.3/Bio/GenBank/__init__.py", 
line 1361, in __getitem__
     handle = self.db[id]
   File 
"/usr/local/src/py_bioinformatics/biopython-1.30/build/lib.linux-i686-2.3/Bio/config/DBRegistry.py", 
line 89, in __getitem__
     return self._get(key)
   File 
"/usr/local/src/py_bioinformatics/biopython-1.30/build/lib.linux-i686-2.3/Bio/config/_support.py", 
line 107, in __call__
     return self.fn(*args, **keywds)
   File 
"/usr/local/src/py_bioinformatics/biopython-1.30/build/lib.linux-i686-2.3/Bio/config/DBRegistry.py", 
line 372, in _get
     handle = self._check_for_errors(handle, self.failure_cases)
   File 
"/usr/local/src/py_bioinformatics/biopython-1.30/build/lib.linux-i686-2.3/Bio/config/DBRegistry.py", 
line 246, in _check_for_errors
     raise KeyError, errormsg
KeyError: "I got HTML and shouldn't have"



TIA,
Kael

--

Kael Fischer, Ph.D.
DeRisi Lab, University of California San Francisco
http://derisilab.ucsf.edu
Desk: 415-514-4320
kael at derisilab.ucsf.edu
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