[BioPython] New User problem with GenBank
JP Glutting
jpg at research.dfci.harvard.edu
Wed Sep 10 13:19:13 EDT 2003
I am having some trouble with a script that I wrote to retrieve GenBank
data.
If I run this (I am just inserting a known GI [33413925]) for a protein
I ran this on a few months ago:
>>> from Bio import GenBank
>>> gi = 33413925
>>> record_parser = GenBank.FeatureParser()
>>> ncbi_dict = GenBank.NCBIDictionary(database="Protein")
>>> ncbi_parse_dict = GenBank.NCBIDictionary(database="Protein",
parser=record_parser)
>>> gb_record = ncbi_dict[gi]
Traceback (most recent call last):
File "<stdin>", line 1, in ?
File "/usr/lib/python2.2/site-packages/Bio/GenBank/__init__.py", line
1538, in __getitem__
raise KeyError, x
KeyError: ERROR, possibly because id not available?
Any idea why this happens, and if there is a work-around?
Thanks,
JP
Peter Bienstman wrote:
> FYI, I've confirmed that the parsing errors don't occur with the current CVS
> version, so the fix should be in the upcoming new release.
>
> Cheers,
>
> Peter
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