[BioPython] GenBank records

[JINLING HUANG]

Jeff,

Thanks a lot. It is working now.

Best wishes,

Jinling


On Tue, 25 Feb 2003, Jeffrey Chang wrote:

> Yes, Rob Knight just reported this bug.  The default NCBIDictionary
> only works for nucleotide sequences.  For protein sequences, you'd need
> to set some parameters.  Try:
> nucleotide_ncbi_dict = GenBank.NCBIDictionary()
> protein_ncbi_dict = GenBank.NCBIDictionary(database="protein",
> format="gp")
>
> And use the protein_ncbi_dict to retrieve protein sequences.
>
> Jeff
>
>
>
> On Tuesday, February 25, 2003, at 12:22 PM, JINLING HUANG wrote:
>
> > Hi, everyone,
> >
> > I am trying to retrieve GenBank records of protein sequences with an
> > old script I wrote before. The script is like the following:
> >
> > from Bio import GenBank
> > import sys
> >
> > file = sys.argv[1]           #file of gi
> > fp1 = open(file, 'r+')
> > ids = fp1.read()
> >
> > lids = ids.split('\n')
> > recNum = len(lids)
> >
> > ncbi_dict = GenBank.NCBIDictionary()
> >
> > for i in range(0, recNum):
> >     gb_record = ncbi_dict[lids[i]]
> >     print gb_record
> >
> >
> > The script works well for records of nucleotide sequences, but does not
> > work for records of protein sequence.  It constantly gives an error
> > message:
> >
> > Traceback (most recent call last):
> >   File "getGBRecords.py", line 24, in ?
> >     gb_record = ncbi_dict[lids[i]]
> >   File
> > "/bio/python2.2/lib/python2.2/site-packages/Bio/GenBank/__init__.py",
> > line
> > 1535, in __getitem__ raise KeyError, x
> > KeyError: ERROR, possibly because id not available?
> >
> >
> > Does anyone know why?  The script was written last summer, do I need to
> > update my biopython to utilize some new features?
> >
> > Thanks and best wishes,
> >
> > Jinling
> >
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>
>