[Biopython-dev] [Bug 2815] Bio.Application command line interfaces

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2815





------- Comment #15 from biopython-bugzilla at maubp.freeserve.co.uk  2009-04-28 13:07 EST -------
(In reply to comment #14)
> > #Don't do this if you want to actually run the application, as
> > #it would only work on Unix where the command is on the path:
> > #cmdline = MafftCommandline()
> > #Instead, use the exe name we determined earlier:
> > cmdline = MafftCommandline(mafft_exe)
> 
> OK, thanks, I'll update the wrappers on my branch.

Have a look at this test_Muscle_tool.py CVS revision 1.4 first:
http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/Tests/test_Muscle_tool.py?cvsroot=biopython

> > If the tools do record their install location in the registry,
> > we can do a win32api call to get the path.  Then if win32api
> > isn't installed just raise the MissingExternalDependencyError
> > exception.
> 
> We can? ;)
> 
> Can you give me some code, ...

There are a lot of ifs here. The code is fairly simple (I've done this kind of
thing before, but can't find an example right away). The catch is establishing
IF the information we want gets written to the registry during the tool
installation or not.

> or I could just use this in the meantime:
> if sys.platform=="win32" :
>     raise MissingExternalDependencyError("Testing with MUSCLE not implemented
> on Windows yet")

Yeah - use something like that, but be aware that the tests shouldn't assume
that the executable name is just "muscle".  Hopefully test_Muscle_tool.py does
this right...

Peter


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