[BioPython] Having some issue with unicode and Bio.PDB

[Michiel De Hoon]

To find out if this is a problem with Biopython, or a problem with Python
itself, can you try:
>>> import array
without Biopython? My guess is that you will find the same error:

ImportError: /users2/invites/wong/apps/lib/python2.4/lib-dynload/array.so:
undefined symbol: _PyArg_NoKeywords

--Michiel.

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



-----Original Message-----
From: WONG Hua [mailto:wong at ebgm.jussieu.fr]
Sent: Tue 10/4/2005 4:35 AM
To: Michiel De Hoon; biopython at biopython.org
Subject: Re: [BioPython] Having some issue with unicode and Bio.PDB
 
After your mail, I cleaned up my pythons and re-builded every modules using
python 2.4.

Now, instead of the previous error, it gives me:
###############################################################
Traceback (most recent call last):
  File "exportPDBv1_0.py", line 6, in ?
  File
"/users2/invites/wong/apps/lib/python2.4/site-packages/Bio/PDB/__init__.py",
line 22, in ?
    from Polypeptide import PPBuilder, CaPPBuilder, is_aa, standard_aa_names
  File
"/users2/invites/wong/apps/lib/python2.4/site-packages/Bio/PDB/Polypeptide.py
", line 5, in ?
    from Bio.Seq import Seq
  File "/users2/invites/wong/apps/lib/python2.4/site-packages/Bio/Seq.py",
line1, in ?
    import string, array
ImportError: /users2/invites/wong/apps/lib/python2.4/lib-dynload/array.so:
undefined symbol: _PyArg_NoKeywords
###############################################################

It does this when I import Bio.PDB. Not when I import Bio only.


On Mon, Oct 03, 2005 at 11:58:20AM -0400, Michiel De Hoon wrote:
>   File
>
"/users2/invites/wong/apps/lib/python2.3/site-packages/Bio/PDB/__init__.py",
> line 22, in ?
>     from Polypeptide import PPBuilder, CaPPBuilder, is_aa,
standard_aa_names
>   File
>
"/users2/invites/wong/apps/lib/python2.3/site-packages/Bio/PDB/Polypeptide.py
> ",
> line 5, in ?
>     from Bio.Seq import Seq
>   File "/users2/invites/wong/apps/lib/python2.3/site-packages/Bio/Seq.py",
> line1, in ?
>     import string, array
> ImportError: /users2/invites/wong/apps/lib/python2.4/lib-dynload/array.so:
> undefined symbol: PyUnicodeUCS2_FromUnicode
> 
> 
> You are mixing python2.3 and python2.4 (see the paths in the traceout). You
> should reinstall Biopython with python2.4. From the traceback, it seems
that
> you have Biopython for python2.3 (or, for some reason, python imports
> python2.3's Biopython instead of python2.4's Biopython).
> 
> --Michiel.