[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 #26 from cymon.cox at gmail.com  2009-05-07 10:39 EST -------
(In reply to comment #25)
> (In reply to comment #24)
> > (In reply to comment #23)
> > > In Prank, should realbranches take no arguments?  i.e. use the new _Switch
> > > class?
> > 
> > Yes, verified and done; pushed to applic-int branch.
> > C.
> 
> Thanks for checking - that's done in CVS now.
> 
> 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)

> 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.


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