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

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Fri May 8 12:07:03 UTC 2009


------- Comment #28 from cymon.cox at gmail.com  2009-05-08 08:07 EST -------
(In reply to comment #27)
> (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?

That's everything currently written. I still want to add interfaces to ProbCons
and T-Coffee.

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

Yes, I'll do that.

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