[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 #9 from cymon.cox at gmail.com  2009-04-28 11:25 EST -------
(In reply to comment #8)
> I've checked the MUSCLE wrapper into CVS, and added the -diags option.

You pulled this from the applic-int branch yes? (Hmm, missed that -diags...)

  I also
> created test_Muscle_tool.py which requires MUSCLE be installed, and checks we
> can invoke it and parse its clustal output OK.

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. 

> A more general alignment wrapper unit test can simply construct some command
> line objects and check them against an expected string (without requiring the
> tools to be installed).

I will do these - all in one test_ApplicationCommandlines.py unittest suite.

> Note that I am concerned about the file exists check on the input file
> argument.  This is helpful, but also prevents certain reasonable usage examples
> - e.g. the input file is created on the fly and doesn't exist yet, or, the
> command line constructed will be submitted to a cluster where the path will be
> valid (even if the path isn't valid on the local machine where Biopython is
> running).

Good point. Perhaps the os.path.exists on input files needs to be dropped from
all wrappers.

> 
> 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.

C.


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