[BioPython] os.system problem with clustalw (on Windows)
Emanuel Hey
jodyhey at yahoo.com
Thu Jul 26 15:25:33 UTC 2007
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
>
>
____________________________________________________________________________________
Be a better Globetrotter. Get better travel answers from someone who knows. Yahoo! Answers - Check it out.
http://answers.yahoo.com/dir/?link=list&sid=396545469
More information about the Biopython
mailing list