Hi all, I've added two branches for consideration, in addition to the simpleframe_doc_align branch (about which I sent a separate e-mail).
Note that hours and hours sitting in a plane on the tarmac is a great way to code, sigh. At git://github.com/ctb/pygr.git, branch simpleframe_tests, I've added a bunch of tests that should work but don't. Briefly, http://github.com/ctb/pygr/commit/69ba04ed3cbfa449331926ff55e68765af29854c - tests for a problem where the translationdb can't be attached to querydb for BlastxMappings queried with a simple sequence. http://github.com/ctb/pygr/commit/26fcd30be5616d111ad392eae70a330cf7783956 - tests that only NLMSASlice objects for the query sequence's translations are returned by BlastxMapping.__getitem__; matches BlastMapping.__getitem__ behavior. http://github.com/ctb/pygr/commit/281eee8b2bf8ab42a36181ea16959d52a29863c8 - basic tests for translationDB behavior, including slicing. http://github.com/ctb/pygr/commit/4dadd8b241bf1494f439cfa9e2b9eb0c349237e5 - test demonstrating a confusing issue where the repr of TranslationDB sequences is identical to the repr of the origin sequence. (NO FIX.) http://github.com/ctb/pygr/commit/54f625858011ab3991ed4ce8ff4338f2794ae16b - tests that BlastxMapping.__getitem__ does not return a consumable iterator or generator. I put this in place Back When but it doesn't match BlastMapping.__getitem__ behavior, and hence is confusing. You should be able to check out this branch and verify that all of these tests fail. Associated fixes (except for the repr issue, which I think calls for a proposal from Chris ;) are in the 'simpleframe_blast_fixes' branch. I think Chris needs to be the one to review these, and, once reviewed and accepted/rejected, the simpleframe branch should be merged into master. --titus -- C. Titus Brown, [email protected] --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
