[BioPython] Clustalw error: .aln not produced

[Peter]

On Feb 8, 2008 5:07 PM, Roger Barrette <rwbarrette at gmail.com> wrote:
> Hey all,
>
> I'm trying to run clustalw from python (windows) using the simple script
> example below;
> ...
> I do have the clustalw executable in the path, and when I copy the generated
> command line for clustalw into the windows command line, it runs fine, and
> generates the alignment, with no errors.
>
> I updated the clustalw _init_ file, but the error still remains.  Any
> thoughts or suggestions would be greatly appreciated.  Thanks.

Are you sure you are using the latest Bio/Clustalw/__init__.py from
CVS?  I would have expected it to try a command line like:

clustalw -INFILE=c:\adenotest.fasta -OUTFILE=c:\adeno4.aln

What version of clustalw do you have (in case that makes a difference)?
Have you tried supplying the full path to the clustalw.exe file?

Peter