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Bug#: 202602
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Status: RESOLVED
Resolution: FIXED
Assigned To: Olivier Fisette <ribosome@gentoo.org>
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Reporter: JTRiley <justin.t.riley@gmail.com>
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Filename Description Type Creator Created Size Actions
biopython-1.44-sequtils-complement.patch Bio.SeqUtils patch for biopython 1.44 patch JTRiley 2007-12-17 18:10 0000 1.01 KB Details | Diff
biopython-1.44.ebuild ebuild for biopython-1.44 using the patch text/plain JTRiley 2007-12-17 18:18 0000 1.25 KB Details
biopython-1.43-sequtils-complement.patch biopython 1.43 Bio.SeqUtils patch patch JTRiley 2007-12-17 18:31 0000 584 bytes Details | Diff
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Bug 202602 depends on: Show dependency tree
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Description:   Opened: 2007-12-17 18:08 0000 
In Biopython 1.43 and 1.44 if you try to use six_frame_translations function
from the Bio.SeqUtils module, you'll get an error: "global name 'complement' is
not defined". 

I submitted a bug (http://bugzilla.open-bio.org/show_bug.cgi?id=2419) upstream
and they responded with a fix from cvs. 

I've created a patch for Biopython 1.43 in portage as well as bumped the ebuild
(and kdtree patch) to 1.44.  Ebuilds/patches are attached. 

I can verify that the patch works for both 1.43 and 1.44 ebuilds on amd64 and
~amd64.  

~jtriley

------- Comment #1 From JTRiley 2007-12-17 18:10:04 0000 ------- 
Created an attachment (id=138748) [details]
Bio.SeqUtils patch for biopython 1.44

------- Comment #2 From JTRiley 2007-12-17 18:18:30 0000 ------- 
Created an attachment (id=138754) [details]
ebuild for biopython-1.44 using the patch

copy biopython-1.43-kdtree.patch to biopython-1.44-kdtree.patch in the files
directory.  you also need to have biopython-1.44-sequtils-complement.patch in
the files directory for this build to work.

------- Comment #3 From JTRiley 2007-12-17 18:31:20 0000 ------- 
Created an attachment (id=138757) [details]
biopython 1.43 Bio.SeqUtils patch 

This patch uses the solution I mention about pasting a complement function
here: http://bugzilla.open-bio.org/show_bug.cgi?id=2419

This is NOT the preferred solution but the patch from cvs only works with the
latest 1.44 version (or at least I can't get it to work with 1.43 :D

------- Comment #4 From Olivier Fisette 2008-01-30 03:34:34 0000 ------- 
BioPython 1.44 (and patch) in CVS. I removed version 1.43. Thanks for your
work.
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