[BioPython] ClustalW problem upwards Biopython 1.43

[Peter]

Stephanie wrote:
>
>>>> print str(cline)
>
> clustalw  pb.fasta -OUTFILE=test2.aln
>
> I'm using CLUSTAL W 2.0.

Are you sure?  The Clustal W 2.0 executable is normally called
clustalw2.exe rather than clustalw.exe - so based on the command line
above I would have expect Clustalw 1.x to be used.  Maybe you have
both versions of ClustalW installed?

Could you tell me where exactly (full paths) you have Clustalw.exe
and/or Clustalw2.exe installed?  This would be helpful for the new
unit test I'm working on.

> Under DOS everything works fine.

I've been having "fun" trying to get a new unit test for this to work
nicely on Windows - there a certainly some combinations of file name
arguments with spaces etc which won't work on Biopython 1.48.  I found
examples where the command line string ran "by hand" at the "DOS"
prompt worked fine, but would fail when invoked in python via os.popen
- on the bright side, using subprocess.Popen instead works much better
(although this isn't available for python 2.3).

If you want to try this new code, I would suggest you first install
Biopython 1.48, and then backup and update
C:\Python25\Lib\site-packages\Bio\Clustalw\__init__.py to revision
1.25 from CVS which you can download here (should be updated within
the hour):
http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/Bio/Clustalw/__init__.py?cvsroot=biopython

Thanks!

Peter