[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 #18 from biopython-bugzilla at maubp.freeserve.co.uk  2009-04-28 14:28 EST -------
(In reply to comment #17)
> 
> OK, pushed to applic-int updated unittest for PRANK, MAFFT, and DIALIGN -
> skipping tests on windows.
> 
> Also changed the names to test_XXXX_tool.py
> 
> C.

Great.  In addition to the MUSCLE and ClustalW stuff, I've got the PRANK code
and unit tests in CVS now.  These three tests all work on a Linux, Mac and
Windows machine (with Python 2.4, 2.5 and 2.6).  I'm stopping working on this
for today.

It would be great if you could test a clean checkout from CVS, and we'll resume
this merge later on for the remaining tools MAFFT and DIALIGN.

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).

Peter


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