[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 #11 from biopython-bugzilla at maubp.freeserve.co.uk  2009-04-28 12:18 EST -------
(In reply to comment #9)
> 
> Ive also just checked in (to the github branch) some unittests for MUSCLE,
> MAFFT, PRANK, and DIALIGN. These just check that the app runs and the return
> code is 0 - a few other checks are made but not much else. 
> 

I think I was looking at your master branch, rather than the applic-int branch:
http://github.com/cymon/biopython-github-master/commits/applic-int
I see the changes now...

> > Also, perhaps we should think about Bio.Application including automatic
> > quoting for filenames with spaces in them... see the _escape_filename
> > function used in Bio.Clustalw and Bio.Blast.NCBIStandalone.  This would
> > be only for parameters explicitly tagged as filenames.
> 
> Yes, I thought about doing that but havent acted.

Seeing as we both think this makes sense, I've done that in CVS.

Peter


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