[BioPython] AttributeError: 'module' object has no attribute 'parse'

[I. Friedberg]

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
>
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> BioPython mailing list  -  BioPython at lists.open-bio.org
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>



-- 

I. Friedberg

"The only problem with troubleshooting is that
sometimes trouble shoots back."