[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
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Attachment #1272 is|0                           |1
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------- Comment #4 from biopython-bugzilla at maubp.freeserve.co.uk  2009-04-02 07:00 EST -------
Created an attachment (id=1273)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=1273&action=view)
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.

Peter


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