[BioPython] Error retrieving from GenBank
Sebastian Bassi
sbassi at gmail.com
Fri Feb 23 21:34:58 UTC 2007
Hello,
Is this biopython bug or just a connexion problem from my side? My
internet connexion is not good, but this problems sounds like
biopython not interacting with eutils.
>>> from Bio import GenBank
>>> gilist=GenBank.search_for("beta-conglycinin")
Traceback (most recent call last):
File "<stdin>", line 1, in ?
File "/usr/lib/python2.4/site-packages/Bio/GenBank/__init__.py",
line 1890, in search_for
ids.append(db_id.dbids.ids[0])
File "/usr/lib/python2.4/site-packages/Bio/EUtils/DBIdsClient.py",
line 124, in _get_dbids
infile = self.efetch(retmode = "text", rettype = "uilist")
File "/usr/lib/python2.4/site-packages/Bio/EUtils/DBIdsClient.py",
line 150, in efetch
complexity = complexity)
File "/usr/lib/python2.4/site-packages/Bio/EUtils/ThinClient.py",
line 987, in efetch_using_dbids
query = {"id": id_string,
File "/usr/lib/python2.4/site-packages/Bio/EUtils/ThinClient.py",
line 644, in _get
return self.opener.open(url)
File "/usr/lib/python2.4/urllib2.py", line 358, in open
response = self._open(req, data)
File "/usr/lib/python2.4/urllib2.py", line 376, in _open
'_open', req)
File "/usr/lib/python2.4/urllib2.py", line 337, in _call_chain
result = func(*args)
File "/usr/lib/python2.4/urllib2.py", line 1021, in http_open
return self.do_open(httplib.HTTPConnection, req)
File "/usr/lib/python2.4/urllib2.py", line 996, in do_open
raise URLError(err)
urllib2.URLError: <urlopen error (-2, 'Name or service not known')>
>>>
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