[BioPython] ClustaW problem upwards Biopython 1.43

[Stefanie Lück]

Hi!

>>> print str(cline)
clustalw  pb.fasta -OUTFILE=test2.aln

I'm using CLUSTAL W 2.0.

Under DOS everything works fine.

Regards
Stefanie


----- Original Message ----- 
From: "Peter" <biopython at maubp.freeserve.co.uk>
To: "Stefanie Lück" <lueck at ipk-gatersleben.de>
Cc: <biopython at lists.open-bio.org>
Sent: Monday, October 27, 2008 4:12 PM
Subject: Re: [BioPython] ClustaW problem upwards Biopython 1.43


On Mon, Oct 27, 2008 at 1:43 PM, Stefanie Lück <lueck at ipk-gatersleben.de> 
wrote:
> Hi!
>
> I just releazed, that a ClustalW alignment gives an error message under 
> Biopython 1.44 and 1.47 whereas under 1.43 everything works fine.
>
> The message is the following (example of the tutorial):
>
> Traceback (most recent call last):
>  File "I:\Final\pair_align.py", line 90, in pair_align
>    alignment = Clustalw.do_alignment(cline)
>  File "C:\Python25\Lib\site-packages\Bio\Clustalw\__init__.py", line 79, 
> in do_alignment
>    status = run_clust.close()
> IOError: [Errno 0] Error
>
> Does someone know what's the problem?

There were some changes made between Biopython 1.43 and 1.44 to try
and deal with spaces in filenames.  Could you do:

print str(cline)

That should show the exact command line python is trying to run.  What
happens if you try this command at the "DOS" prompt?

Also, what version of clustalw do you have installed?

Thanks,

Peter