[BioPython] NCBIDictionary and genome database
Michiel Jan Laurens de Hoon
mdehoon at c2b2.columbia.edu
Thu Jan 25 20:27:20 UTC 2007
Hi Tiago,
Which genbank record are you trying to download?
Just so I can replicate the problem and try your workaround.
--Michiel
Tiago Antão wrote:
> Hi!
>
> Just a question regarding accessing NCBI genome database from NCBIDictionary:
> In the code there is:
> class NCBIDictionary:
> """Access GenBank using a read-only dictionary interface.
> """
> VALID_DATABASES = ['nucleotide', 'protein']
> That is, genome is not a valid one.
> Is there a reason for that?
>
> BTW, I have the following workaround (which might be good or bad...):
>
> from Bio import GenBank
> from Bio.config.DBRegistry import EUtilsDB, DBGroup
> from Bio.dbdefs.genbank import ncbi_failures
> from Bio import db
>
> genome_genbank_eutils = EUtilsDB(
> name = "genome-genbank-eutils",
> doc = "Retrieve genome GenBank sequences from NCBI using EUtils",
> delay = 5.0,
> db = "genome",
> rettype = "gb",
> failure_cases = ncbi_failures
> )
>
>
> ncbi_dict = GenBank.NCBIDictionary('nucleotide', 'genbank')
> ncbi_dict.db = genome_genbank_eutils
>
> Regards,
> Tiago
--
Michiel de Hoon
Center for Computational Biology and Bioinformatics
Columbia University
1130 St Nicholas Avenue
New York, NY 10032
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