[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 #8 from biopython-bugzilla at maubp.freeserve.co.uk  2009-04-28 11:04 EST -------
I've checked the MUSCLE wrapper into CVS, and added the -diags option.  I also
created test_Muscle_tool.py which requires MUSCLE be installed, and checks we
can invoke it and parse its clustal output OK.

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).

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).

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.


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