[BioPython] os.system problem with clustalw

[Emanuel Hey]

Peter

Thanks.  

Actually do_alignment() is not working for me for just
names,  even without directories. 

>>> cline = MultipleAlignCL('data.faa')
>>> str(cline)
'clustalw -INFILE=data.faa'
>>> align = do_alignment(cline)
Traceback (most recent call last):
  File "<pyshell#6>", line 1, in <module>
    align = 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 data.aln not produced,
commandline: clustalw -INFILE=data.faa


Is this me?  I think I got the new __init__.py
installed ok. 

jhey

--- Peter <biopython at maubp.freeserve.co.uk> wrote:

> Emanuel Hey wrote:
> > Thanks much for responding
> > 
> > ok,  I had no idea Clustalw was so particular
> about its command line
> > flags.
> 
> Its confused me in the past too!
> 
> > I was not using Bio.Clustalw to build the command
> line because I
> > could not get that to work either.
> 
> Ahh. Good point. I guess I should have checked this
> when I wrote my last
> email, but it turns out Bio.Clustalw was building
> it's command lines
> without using the INPUT argument... which I've just
> fixed in CVS.
> 
> This should now work:
> 
> from Bio.Clustalw import MultipleAlignCL,
> do_alignment
> faa_filename =
> 'C:\\temp\\pythonplay\\hcgplay\\data.faa'
> cline = MultipleAlignCL(faa_filename)
> #print cline
> align = do_alignment(cline)
> for col_index in range(align.get_alignment_length())
> :
>      print align.get_column(col_index)
> 
> Please try this by backing up and then updating the
> file
> Bio/Clustalw/__init__.py to CVS revision 1.15, which
> you can download here:
> 
>
http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/Bio/Clustalw/__init__.py?cvsroot=biopython
> 
> Thanks
> 
> Peter
> 



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