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 attachment 138748 [details, diff] Bio.SeqUtils patch for biopython 1.44
Created attachment 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 attachment 138757 [details, diff] 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.
