[BioPython] clustalw problem using standalone or Bio.Clustalw

[Emanuel Hey]

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')

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


Thanks much for any pointers

jhey


       
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