[BioPython] NCBIDictionary and genome database

[Tiago Antão]

Hi,

I am trying to download complete genomes, not nuclear but
mithocondrial (~17000 bps each).
For instance:

parser = GenBank.FeatureParser()
ncbi_dict = GenBank.NCBIDictionary('nucleotide', 'genbank', parser=parser)
ncbi_dict.db = genome_genbank_eutils
res = GenBank.search_for('txid8292[orgn]', 'genome')
gb_entry = ncbi_dict[res[0]]

In this case I am searching_for all amphibian genomes query: txid8292[orgn]
Or, using the web:
http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=8292&lvl=0
And Choose "Genome Sequences" on the right (73):
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Genome&cmd=Search&dopt=DocSum&term=txid8292[Organism:exp]


On 1/25/07, Michiel Jan Laurens de Hoon <mdehoon at c2b2.columbia.edu> wrote:
> 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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