[Biopython-dev] [Bug 2508] NCBIStandalone.blastall: provide support for '-F F' and make it safe

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2508





------- Comment #5 from mmokrejs at ribosome.natur.cuni.cz  2008-06-23 06:56 EST -------
(In reply to comment #4)

Yes, the "filter" argument is not clear, please improve the docs in the sources
and on the web. At the best I would in addition propose renaming the argument.

Regarding the patch in comment #3, I think it should be more strict and blast*
functions should only accept explicitly listed arguments in the function
definition, so no kwargs, etc. But it is a good startup. In general, I would
propose to provide a general wrapper function to be placed in front of _ALL_
popen3() calls. And, conjuction, replace the popen3 calls with
subprocess.Popen. See Bug #2528 on the NCBIStandalone.blastall() where is a
working example of this.


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