[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 #21 from biopython-bugzilla at maubp.freeserve.co.uk  2009-04-29 07:40 EST -------
(In reply to comment #20)
> (In reply to comment #18)
> > (In reply to comment #17)
> > Also, would you be able to look into making the Prank test faster to run?
> > Maybe use a smaller example input file?  After we do that, I'd like to
> > use it to test the Nexus parser via Bio.AlignIO (just something simple
> > which won't be affected by gap differences between different versions of
> > PRANK - like my tests for MUSCLE).
> 
> Reduced run time from 8s to 1s, added asserts for Nexus outfile parsing.
> 
> Pushed to applic-int
> C.

Lovely - checked into CVS.  On the Linux machine I tested this on it went from
16s to 2s :) 

P.S. See also Bug 2822 for some of my ideas on making the Bio.Application base
class easier to use.


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