[BioPython] GenBank records

[JINLING HUANG]

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