[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 #27 from biopython-bugzilla at maubp.freeserve.co.uk  2009-05-07 11:22 EST -------
(In reply to comment #26)
> > I think the final bit of new code is _Dialign.py which still needs to be
> > updated for the new style __init__ method.
> 
> Done - pushed to applic-int (Note windows path stuff absent from _Dialign)
> 

OK, that is in CVS now.

> > Then there are your unit tests...
> 
> As they are at present, unittests for Muscle, Mafft, Dialign and Prank all
> pass. They could of course be made arbitrarily more complex... they should
> probably have at least one test that uses the properties style parameter
> setting rather than just set_paramter()
> C.

I've added test_Dialign_tool.py to CVS, and then switched a few to using
keyword arguments and properties.  As far as I can see from here, the tool
isn't expected to work on Windows (although it might still be possible with
cygwin):
http://bibiserv.techfak.uni-bielefeld.de/download/tools/DIALIGN_221.html

Is that everything?  You'd mentioned a more general test which just builds the
strings, but doesn't actually need to run any of the tools themselves.


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