[Biopython] index_db problem

[Peter Cock]

On Tue, Nov 15, 2011 at 12:28 PM, natassa <natassa_g_2000 at yahoo.com> wrote:
> Hi,
>
> I have a problem with a script using the Bio.SeqIO index_db function:
> I have previously it successfully, but as I  had to recently change
> computers I now tried the same  script with no success. I get the error:
>
> AttributeError: 'module' object has no attribute 'index_db'
>
> although I have installed biopython 1.58 (the index_db is apparently
> from 1.57 and on, and on the pevious computer I had installed the
> 1.57). I checked if i have sqlite 3 by importing the module, and this
> seems OK. So now i am kind of stuck why the module SeqIO from
> 1.58 gets imported, but not the function.
>
> My function using it is something like:
> ...
>
> and i have python 2.6
>
> Any help would be appreciated!
> Thank you,
>
> Anastasia

It sounds like you're getting Biopython 1.57 even if 1.58 is also
installed somewhere else. Try this to find out which is being
used and where it is installed:

import Bio
print Bio.__version__
print Bio.__file__
from Bio import SeqIO
print SeqIO.__file__

Peter