[Biopython-dev] [Bug 2528] New: 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

           Summary: NCBIStandalone.blastall(): Replace os.popen3 with
                    subprocess.Popen
           Product: Biopython
           Version: 1.45
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: mmokrejs at ribosome.natur.cuni.cz


I have already mentioned this on the email list few weeks ago ... NCBI Blast
2.2.18 (but was a case of also previous version as far as I remember) does not
flush output buffers when run from under mod_python-3.3.11/apache-2.2.8.

I tried to flush the buffers or disable buffering but it does not help. In the
end, a working solution is to move the using subprocess module introduced in
python 2.4 and which deprecates os.system, os.exec, os.popen* and other
functions. The following patch works for me, so the user receives back into
his/her web browser the blast stdout. Somehow, one has to copy the data into
another variable and close the file descriptors used by blastall binary.


Unfortunately, still a stale process can be seen in "ps -ef" output:
apache    5382  5323 47 12:31 ?        00:00:04 [blastall] <defunct>

But as I have said, at least the data is not buffered anymore.


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