[BioPython] os.system problem with clustalw (on Windows)

[Emanuel Hey]

Peter

both of these now work. 

>>> faa_filename = 'data.faa'
>>> cline = MultipleAlignCL(faa_filename)
>>> align = do_alignment(cline)
>>> 
>>> faa_filename =
'C:\\temp\\pythonplay\\hcgplay\\data.faa'
>>> cline = MultipleAlignCL(faa_filename)
>>> align = do_alignment(cline)

Thanks!

jhey

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

> Emanuel Hey wrote:
> > Peter
> > 
> > Thanks.  
> > 
> > Actually do_alignment() is not working for me for
> just
> > names,  even without directories. 
> 
> My fault maybe.  The old version of
> Bio/Clustalw/__init__.py before my 
> first update today probably would have worked
> without directories in the 
> filename.
> 
> My mistake was that while clustalw on windows seems
> to copes with / or - 
> for some of its options, it has to be /infile=...
> rather than 
> -infile=... (using either infile for INFILE is
> fine). On Linux, you can 
> only use - for arguments.
> 
> I should have spotted there was something amiss, but
> I was tricked by 
> the fact that in my simple testing the output
> alignment already existed, 
> and there was no error trapped from the system call,
> so it appeared to 
> work.  Grr.
> 
> There are also "complications" when filenames
> contain spaces (a 
> Microsoft innovation which frankly was in many
> respects a dreadful idea).
> 
> Emanuel - please could you try updating
> Bio/Clustalw/__init__.py once 
> again, trying the do_alignment() function, and
> reporting back. Please be 
> explicit about the filenames used.
> 
> Peter
> 
> 



       
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