[Biopython-dev] [Bug 2804] Clustalw subprocess hangs when large stdout returned

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2804





------- Comment #6 from biopython-bugzilla at maubp.freeserve.co.uk  2009-04-02 10:34 EST -------
I've updated test_Clustalw_tool.py in CVS to catch this dead lock, and
confirmed the unit test will fail on Mac and Linux when using subprocess (on
the bright side, Python 2.3 should still work), but the test passes with the
fix outlined - or simply using the os.popen code instead.

Interestingly the lockup seems to happen more readily on Linux that on the Mac.
I've yet to test on Windows.

I also added three tests for standard error conditions - interestingly I don't
ever seem to get an error code back (either with subprocess or os.popen).  What
about you?  This makes testing these special cases for raising specific IOError
exceptions difficult.


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