[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


biopython-bugzilla at maubp.freeserve.co.uk changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         OS/Version|Linux                       |All
         Resolution|                            |FIXED




------- Comment #7 from biopython-bugzilla at maubp.freeserve.co.uk  2009-04-02 11:19 EST -------
Hi Cymon,

I've updated the unit test for Windows on Python 2.3 through 2.6 (had to move
some file deletions to the end, and watch out for extra error message
variations).

Windows also deadlocks on this example when using subprocess - the test should
normally take about four seconds in total (depending on your computer's speed
of course).  Using os.popen avoids the deadlock (but can't cope with file names
with spaces).  Your fix in comment 5 also works :)

So, now we have a unit test which catches this deadlock on all three operating
systems, which confirms your fix which works on all three.  I've checked it
into CVS, and marked this bug as fixed.

[I'm still not sure what is happening with the return values - if you look into
this further please raise a new bug for it.]

Thanks!

Peter


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