[BioPython] from Bio import db

[Michiel De Hoon]

Dear Eric,

Some significant changes were needed in Biopython release 1.44 for reasons of
compatibility with the new version of mxTextTools. Unfortunately, as you
found, some code may break as a result.

In your code:
>   File "/home/eric/workspace/PySeq/src/GenbankSearch.py", line 18, in
<module>
>    parser = record_parser)
>   File "/usr/lib64/python2.5/site-packages/Bio/GenBank/__init__.py",
>   line 1283, in __init__
>     from Bio import db
> ImportError: cannot import name db

It looks like we missed an "import db" statement in Bio/GenBank/__init__.py.
Can you show us the code leading up to this point? I'm guessing that you are
trying to use NCBIDictionary, but it would be helpful to see how exactly you
are trying to use it, so that we can come up with a solution.

Sorry for the trouble.

--Michiel.




Michiel de Hoon
Center for Computational Biology and Bioinformatics
Columbia University
1150 St Nicholas Avenue
New York, NY 10032



-----Original Message-----
From: biopython-bounces at lists.open-bio.org on behalf of Eric Gibert
Sent: Wed 11/7/2007 8:50 PM
To: biopython at lists.open-bio.org
Subject: [BioPython] from Bio import db
 
Hello,

I just upgraded to BioPython 1.44 and when I try to run my previous script, I
have
 the error:

Traceback (most recent call last):
  File "/home/eric/workspace/PySeq/src/GenbankSearch.py", line 18, in
 <module>
    parser = record_parser)
  File "/usr/lib64/python2.5/site-packages/Bio/GenBank/__init__.py",
 line 1283, in __init__
    from Bio import db
ImportError: cannot import name db


(I am on Fedora 7 64bit)

Any suggestions?

Thank you

Eric



 
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