[BioPython] script to extract records from nucleotide database

[Matthew Abravanel]

Hi Christof and everyone,

Thanks for all the comments and everything, the OS   I am using is NetBSD
3.1 , and I think you were right Peter about my biopython version I think it
was 1.43 instead of the latest 1.44 version.  If I get the latest
1.44version  of biopython do you think the code should work or do I
need to
think of something else?


Sincerely,

                     Matthew

On Nov 13, 2007 3:59 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:

> Christof Winter wrote:
> > Matthew Abravanel wrote:
> >> Hi Christof,
> >>
> >> I tried out the code you sent me just to see if it would work but I get
> an
> >> attribute error or something? Here is the error I get:
> >>
> >> Traceback (most recent call last):
> >>   File "./run", line 3, in ?
> >>     from Bio import GenBank
> >>   File "/usr/pkg/lib/python2.4/site-packages/Bio/GenBank/__init__.py",
> line
> >> 47, in ?
> >>   File "/usr/pkg/lib/python2.4/site-packages/Bio/GenBank/Scanner.py",
> line
> >> 20, in ?
> >>     from Bio.SeqRecord import SeqRecord
> >>   File "/usr/pkg/lib/python2.4/site-packages/Bio/SeqRecord.py", line
> 11, in
> >> ?
> >>   File "/usr/pkg/lib/python2.4/site-packages/Bio/FormatIO.py", line 55,
> in
> >> __init__
> >> AttributeError: 'module' object has no attribute 'formats'
> >
> > Hi Matthew,
> >
> > your import of the GenBank module fails. Most likely your BioPython
> installation
> > is broken. Could you try to re-install it?
>
> What version of Biopython do you have Matthew? I'm pretty sure it isn't
> the latest Biopython 1.44, it must be Biopython 1.43 or older... but
> even on Biopython 1.43 doing "from Bio import GenBank" should work.
>
> Odd.  What OS are you using, and how and where did you install Biopython?
>
> Peter
>
>