[BioPython] Clustalw error: .aln not produced

[Roger Barrette]

Hi Peter,

I'm using the version 1.16 of the clustalw_init_file, and clustalw version
2.0.
I notice that when I run clustalw from the windows command line, it
generates the adeno4.aln file.  After this file is generated, the script
WILL successfully run from python.  It doesn't appear to be able to create a
new file when called from the python script, but it will update and modify
the existing one. Am I not setting up the files correctly?

I'm not sure what you mean by "supply the full path to the
clustalw.exefile".  I have the location of the executable
clustalw.exe described in the system path, and it runs directly from the
windows command line, so I would assume it is properly mapped.  If you mean
the path to the .fasta file and location of the output file for clustalw to
use; they are being input directly at the clustalw command, or am I missing
something?  Thanks.

-Roger


On 2/8/08, Peter <biopython at maubp.freeserve.co.uk> wrote:
>
> 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
>