[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 #3 from cymon.cox at gmail.com  2009-04-01 18:42 EST -------
(In reply to comment #2)
> It is great that you've found a simple and reproduceable test case.  I can
> confirm this problem on a Linux machine with Python 2.4.3 (what version of
> python do you have?)

Python 2.5.2 (r252:60911, Oct  5 2008, 19:24:49)
[GCC 4.3.2] on linux2

on Ubuntu Intrepid


> 
> (In reply to comment #1)
> > Created an attachment (id=1272)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=1272&action=view) [details] [details]
> > clustalw subprocess patch
> 
> Unfortunately the patch is flawed here:
> 
>     status = child_process.communicate()[1]



Actually, the 'whole' patch is good. Have a look at the second bit of the
patch, where I change my initial commit to my branch:

         #Grab stderr
-        status = child_process.communicate()[1]
+        child_process.communicate()
+        value = child_process.returncode
     except ImportError :

etc...


I've been trying to get to grips with git - and clearly havent succeeded to
yet!

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.

Sorry I didnt make that clear.

If anyone knows how to get the diff against only the current file version, I'd
appreciate the answer ;)

Cheers, C.


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