[BioPython] clustalw problem using standalone or Bio.Clustalw
Emanuel Hey
jodyhey at yahoo.com
Tue Jul 24 14:38:56 UTC 2007
Yes, it was indeed a path problem. Thanks.
jhey
--- Peter <biopython at maubp.freeserve.co.uk> wrote:
> 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
>
>
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