[BioPython] AttributeError: 'module' object has no attribute 'parse'
I. Friedberg
idoerg at gmail.com
Tue Jun 12 16:54:30 UTC 2007
I just tried to install biopython in Ubuntu Feisty and the installation
breaks:
% sudo apt-get install python-biopython
[... lots of apt install log messages...]
Setting up python-biopython (1.42-2) ...
Compiling /var/lib/python-support/python2.5/Bio/Wise/dnal.py ...
File "/var/lib/python-support/python2.5/Bio/Wise/dnal.py", line 5
from __future__ import division
SyntaxError: from __future__ imports must occur at the beginning of the file
How come you managed to install?
On 6/12/07, richa <richa at musc.edu> wrote:
>
> Hi all,
>
> Just installed biopython on ubuntu feisty. Dependencies and package
> seemed to install without a problem. Many of the test files that come
> with it work fine, but the SeqIO object runs into a problem. For
> example, the following code causes an error saying that the 'module'
> object has no attribute 'parse'.
>
> Is this a problem of syntax or is it an installation issue?
>
> from Bio import SeqIO
> handle = open("ls_orchid.fasta", "rU")
> for record in SeqIO.parse(handle, "fasta") :
> print record.id
>
> _______________________________________________
> BioPython mailing list - BioPython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>
--
I. Friedberg
"The only problem with troubleshooting is that
sometimes trouble shoots back."
More information about the Biopython
mailing list