[BioPython] GenBank.NCBIDictionary 'Operation timed out'
David Moreira
david.moreira at u-psud.fr
Wed May 14 09:26:13 UTC 2008
Dear all,
I have a problem when using the GenBank.NCBIDictionary to retrieve
sequences from GenBank. Quite often my script finishes with an error due
to a too long connexion time:
urllib2.URLError: <urlopen error <10060, 'Operation timed out'>>
The code I am using is very simple, I have tried to avoid the problem by
waiting 10 seconds before retrying, but it does not work:
def retrieve_taxonomy_seq(acc_number):
# retrieve the sequence from GenBank
try:
ncbi_dict = GenBank.NCBIDictionary(database="nucleotide",
format="genbank")
# exception in case of network problems
except IOError:
print "Network down, waiting 10 seconds before continuing"
time.sleep(10)
retrieve_taxonomy(acc_number)
I have to use this function about ~100 times. I know that the best would
be to have a local data base to avoid Internet connexion problems, but
by some practical reasons I prefer to go directly to GenBank for my search.
Do you have any suggestion to avoid this problem?
Best,
David
--
David MOREIRA
Unité d'Ecologie, Systématique et Evolution - UMR CNRS 8079
Université Paris-Sud. Bâtiment 360. 91405 Orsay CEDEX. FRANCE
Tel: 33 1 69 15 76 08 Fax: 33 1 69 15 46 97
http://www.ese.u-psud.fr/microbiologie/
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