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

[Peter]

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