[BioPython] GenBank.NCBIDictionary 'Operation timed out'

[Peter]

On Wed, May 14, 2008 at 10:26 AM, David Moreira <david.moreira at u-psud.fr> wrote:
> 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'>>

That does sound like a network problem.  Perhaps you can do some
investigation like running ping on the NCBI host when you have issues,
or consult your IT helpdesk to see if there are any local issues.

Which version of Biopython are you using?  In Biopython 1.45 we
switched the NCBIDictionary class from using EUtils to using Entrez
internally.

>  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?

Have you added a local cache to record the sequences on your hard disk
once they are downloaded, to avoid re-downloading the same things many
times?

Peter