[Biopython] pro

Björn Johansson bjorn_johansson at bio.uminho.pt
Mon Apr 5 13:50:25 UTC 2010


Hi,
I have a problem that may be related to biopython (or not).
I have written a plugin for a cross platform program (Wikidpad) that relies
on some biopython modules.
I do the development on ubuntu 9.10 and have Wikidpad installed using wine
to be able to test the functionality on windows.

Under wine I have added the following code to make biopython installed under
linux  available to the python interpreter (py2exe) under wine:

if sys.platform == 'win32':
    sys.path.append("z:\usr\local\lib\python2.6\dist-packages")
    sys.path.append("z:\usr\lib/python2.6")

line 40 in "SeqTools.py" below reads: from Bio import SeqIO
I get the error below when importing the module under wikidpad running under
wine

  File "C:\Program Files\WikidPad\user_extensions\SeqTools.py", line 40, in
<module>
  File "z:/usr/local/lib/python2.6/dist-packages\Bio\SeqIO\__init__.py",
line 303, in <module>
  File "z:/usr/local/lib/python2.6/dist-packages\Bio\SeqIO\InsdcIO.py", line
29, in <module>
  File "z:/usr/local/lib/python2.6/dist-packages\Bio\GenBank\__init__.py",
line 53, in <module>
  File
"z:/usr/local/lib/python2.6/dist-packages\Bio\GenBank\LocationParser.py",
line 319, in <module>
  File
"z:/usr/local/lib/python2.6/dist-packages\Bio\GenBank\LocationParser.py",
line 177, in __init__
  File "z:/usr/local/lib/python2.6/dist-packages\Bio\Parsers\spark.py", line
88, in __init__
  File "z:/usr/local/lib/python2.6/dist-packages\Bio\Parsers\spark.py", line
129, in collectRules
  File "z:/usr/local/lib/python2.6/dist-packages\Bio\Parsers\spark.py", line
101, in addRule
AttributeError: 'NoneType' object has no attribute 'split'

I wonder if anyone has an immediate idea of what I am doing wrong?
The python interpreter under wine seem to find the biopython modules.
I cannot understand the error that I get afterwards.....

grateful for help!
/bjorn



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