On Jul 15, 2009, at 10:10 PM, C. Titus Brown wrote: > > first, there's an error in blast_test, > > ERROR: test_blastx_parser (blast_test.BlastParsers_Test) > ---------------------------------------------------------------------- > ... > File "/Users/t/dev/pygr/tests/blast_test.py", line 93, in > reformat_results > for t in result.edges(mergeMost=True): > AttributeError: 'pygr.cnestedlist.NLMSA' object has no attribute > 'edges' > > ----------------------------------------------------------------------
Looks like your setup.py is not automatically recompiling cnestedlist.pyx... Just force it to recompile this module. > > second, I've added some tests for reverse-complement matches in BLAST, > branch 'blast_test_rc' that (a) pass and (b) should be merged to your > master. > > http://github.com/ctb/pygr/commit/7fbb8dac62bc6ce337a2e9175a74155be8e95f02 > http://github.com/ctb/pygr/commit/63b4dca337c29b9a9186e5ca48033eb825904721 Awesome! I was thinking that we definitely need some test examples where the homology hits are on the negative strand. All your new tests pass. I merged these to the simpleframe branch, and pushed it back to github. -- Chris --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "pygr-dev" group. To post to this group, send email to [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/pygr-dev?hl=en -~----------~----~----~----~------~----~------~--~---
