Home | Docs | Forums | Lists | Bugs | Planet | Store | GMN | Get Gentoo!

Full Text Bug Listing

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

Created an attachment (id=138748) [details]
Bio.SeqUtils patch for biopython 1.44

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.  

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

BioPython 1.44 (and patch) in CVS. I removed version 1.43. Thanks for your
work.