[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 #5 from cymon.cox at gmail.com  2009-04-02 07:32 EST -------
(In reply to comment #4)
> Created an attachment (id=1273)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=1273&action=view) [details]
> Patch to Bio/Clustalw/__init__.py
> 
> (In reply to comment #3)
> > 
> > When you run the command "git format-patch" it creates a separate for each
> > commit to the branch, and I can't figure out how to just get the patch against
> > only the current version of the file. So git gave me two patches, which I
> > cat'ed together and submitted as a composite patch.
> > 
> 
> I see - that odd looking patch had confused me.  I think you want to look at
> "giff diff ..." for this, it also can do things like show the diff between the
> remote branches.
> 
> I have tested this new patch on both Linux and Mac now, using both ClustalW
> 1.83 and 2.0.10 - next up Windows, and extending the unit test.

Your new patch doesnt indent the lines (as in my original patch):

113         value = 0
114         if status: value = status / 256

so that they only get executed when run_clust = os.popen(str(command_line))

The return code from child_process.communicate() is already /256

also assign value = child_process.returncode (the return code is 0 for success
and never "")

"""
        child_process.communicate()
        value = child_process.returncode
    except ImportError :
        #Fall back for python 2.3
        run_clust = os.popen(str(command_line))
        status = run_clust.close()

        # The exit status is the second byte of the termination status
        # TODO - Check this holds on win32...
        value = 0
        if status: value = status / 256

    # check the return value for errors, as on 1.81 the return value
    # from Clustalw is actually helpful for figuring out errors
    # 1 => bad command line option
    if value == 1:
        raise ValueError("Bad command line option in the command: %s"
                         % str(command_line))

"""

C.


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