[Biopython-dev] [Bug 2528] NCBIStandalone.blastall(): Replace os.popen3 with subprocess.Popen

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2528





------- Comment #2 from biopython-bugzilla at maubp.freeserve.co.uk  2008-06-24 05:38 EST -------
With this patch we have to wait for the sub-process to finish before we can
read its output.  This is a potential drawback as it delays the parsing. 
Currently we should be able to can parse this iteratively as the queries are
processed.

Also, you are loading the entire output into memory (as a list of strings,
which you then turn into a StringIO handle).  This is potentially a very bad
idea, as in extreme cases Blast XML files can be GB in size.

I'm not keen on your solution, but I don't know what to suggest for your
original problem, running Blast under mod_python-3.3.11/apache-2.2.8. 

Two minor points: Do you think we can do anything better on Python 2.3?  Did
you intend something similar for blastpgp and rpsblast.


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