[BioPython] clustalw problem using standalone or Bio.Clustalw

[Peter]

Emanuel Hey wrote:
> I am running windows XP,  Python 2.5.1  and BioPython
> trying to do a multiple alignment on a fasta file.
> The file is not large, with just 10 sequences to try
> things out.  I'm familiar with clustalw as a command
> line program. 
> 
> With clustalw in the path the following works fine and
> opens a command prompt window with the clustalw menu
>>>> os.system('clustalw')

That suggests that clustalw is on the windows path, or in the current 
directory. Great. (I personally use a full path to clustalw.exe when 
working on Windows)

> However this line returns a '1' when it should do an
> alignment on the sequences contained in c.faa
>>>> os.system('clustalw c.faa')

Obvious question time - is the file c.faa in the current directory?
i.e. Does this work?

import os
assert os.path.isfile('c.faa')

> I also tried following the examples in the cookbook
> http://biopython.org/DIST/docs/tutorial/Tutorial.html
> and the examples in the bioinformatics course
> http://www.pasteur.fr/recherche/unites/sis/formation/python/ch11s06.html#quest_run_clustalw
> 
> For example,  the following call to a constructed
> command line 
>>>> alignment = Clustalw.do_alignment(cline)
> 
> generates this error result
> 
> 
> Traceback (most recent call last):
>   File "<pyshell#82>", line 1, in <module>
>     alignment = Clustalw.do_alignment(cline)
>   File "C:\Program
> Files\Python25\Lib\site-packages\Bio\Clustalw\__init__.py",
> line 117, in do_alignment
>     % (out_file, command_line))
> IOError: Output .aln file .\testalign.out not
> produced, commandline: clustalw
> .\chimp_hemoglobin.gb.faa -OUTFILE=.\testalign.out

This may be the same issue...

Could you try using fully qualified paths for both clustalw.exe and the 
input fasta file?

Peter