Bug 202602 – >=sci-biology/biopython-1.43 require a patch to Bio.SeqUtils

• Product: Gentoo Linux
• Status: RESOLVED FIXED

[Description JTRiley 2007-12-17 18:08:42 UTC]

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 JTRiley 2007-12-17 18:10:04 UTC]

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

[Comment 2 JTRiley 2007-12-17 18:18:30 UTC]

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.

[Comment 3 JTRiley 2007-12-17 18:31:20 UTC]

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

[Comment 4 Olivier Fisette (RETIRED) 2008-01-30 03:34:34 UTC]

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