[BioPython] ClustalW problem upwards Biopython 1.43

[Stefanie Lück]

I'm sorry! I'm using CLUSTAL W 1.8. It's my mistake because I work on 
several PC's ;-)

Well, for the full path:
I put the .exe into the folder of my programs because I use it over 
Biopython. So usually I have it on my USB stick (X:\MyProgram\clustalw.exe).

I'll try the code you gave me.

Thanks,
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: Tuesday, October 28, 2008 12:20 PM
Subject: Re: [BioPython] ClustalW problem upwards Biopython 1.43


> 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
>