[BioPython] Clustalw error: .aln not produced

[Roger Barrette]

Hey Peter, I went and downloaded clustalw version 1.83, and that fixed the
problem, so it would appear at least that part of the problem has to do with
clustalw 2.0.  Thanks.

-Roger


On 2/8/08, Roger Barrette <rwbarrette at gmail.com> wrote:
>
> 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
> >
>
>


-- 
Roger William Barrette II, Ph.D
Microbiologist
USDA /APHIS/ VS/ FADDL
Plum Island Animal Disease Center
P.O. Box 848,
Greenport, NY 11944
631-323-3300 (Lab)
631-323-3200  x4415 (Office)
RWBarrette at gmail.com
Roger.W.Barrette at APHIS.USDA.GOV