[BioPython] problem accessing ncbi through GenBank.NCBIDictionary
Peter
biopython at maubp.freeserve.co.uk
Tue Sep 4 13:05:21 UTC 2007
Miguel Ortiz-Lombardía wrote:
> Hello everyone.
>
> I'm trying to retrieve from NCBI a series of GeneBank records from a list
> read from a file.
How many GenBenk identifiers are we talking about? Just trying to get an
idea of the scale of the problem. It certainly sounds like either
network failures or timeouts. Have you try something like this?
from Bio import GenBank
from urllib2 import HTTPError
ncbi_dict = GenBank.NCBIDictionary("protein", "genbank")
ids = ['14598510', '16904191']
output = open('saved.gb','w')
for gbid in ids:
print "Fetching %s" % gbid
try :
gb_record = ncbi_dict[gbid]
except HTTPError, e :
#Check error code?
print str(e)
print "Re-trying %s" % gbid
gb_record = ncbi_dict[gbid]
output.write(gb_record)
output.close()
print "Done"
Peter
More information about the Biopython
mailing list