[BioPython] Clustalw error: .aln not produced

[Roger Barrette]

Hey all,

I'm trying to run clustalw from python (windows) using the simple script
example below;
**
*import os
from Bio.Clustalw import MultipleAlignCL
from Bio.Clustalw import do_alignment
from sys import **
*cline = MultipleAlignCL("c:\\adenotest.fasta")
cline.set_output("c:\\adeno4.aln")
print "Command line: ", cline*
*align = do_alignment(cline)
for seq in align.get_all_seqs():
    print seq.description
    print seq.seq*
**
This generates the command line "clustalw c:\adenotest.fasta
-OUTFILE=c:\adeno4.aln"
**
However, I continuously get the following error message:
*IOError: Output .aln file c:\adeno4.aln not produced, commandline: clustalw
c:\adenotest.fasta -OUTFILE=c:\adeno4.aln*
**
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.

-Roger
**
**