[BioPython] Error retrieving from GenBank

[Julius Lucks]

Hi Sebastian,

It looks like your error occurred within python 2.4's urllib, so it  
might be that.  Otherwise, I am using python 2.5 and got your code to  
work (with a gilist of length 930).  The query took a little while  
(maybe about 3 minutes), so if you have a bad connection, something  
might have timed out.

Julius


-----------------------------------------------------
http://openwetware.org/wiki/User:Lucks
-----------------------------------------------------



On Feb 23, 2007, at 4:34 PM, Sebastian Bassi wrote:

> 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')>
>>>>
>
>
> -- 
> Bioinformatics news: http://www.bioinformatica.info
> Lriser: http://www.linspire.com/lraiser_success.php?serial=318
> _______________________________________________
> BioPython mailing list  -  BioPython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython