On Fri, Jun 05, 2009 at 11:18:02AM -0700, Christopher Lee wrote: -> On May 31, 2009, at 6:50 AM, C. Titus Brown wrote: -> -> > I can't think of a reason why blastx and tblastx shouldn't be able to -> > take in query databases as well as sequences, but that doesn't mean -> > there isn't one ;). Any comments? -> -> Hi Titus, -> I think this makes particular sense in light of your proposal for -> changing the behavior of BlastxMapping, to use "canonical" 6-frame -> translation annotations rather than the original way I did it -> (creating a new TranslationAnnotation for each hit, and returning a -> separate NLMSASlice for each hit). Under your proposal, it seemed we -> would use the same set of canonical TranslationAnnotations for all -> hits to a given sequence, and thus could save them all to the same -> NLMSA. That would make the BlastxMapping interface the same as the -> BlastMapping interface, whose __call__() returns a NLMSA object. -> -> Shall we go ahead and make that change? Do you want to discuss -> details of the implementation? And who should do it?
Hey Chris, great! This is on the top of my list for pygr work, but I'm still struggling a bit with implementation details (not so much "can I get it to work" but more "what's the right way to do it"). I'll send a concrete proposal out to the list when I get chance to build a prototype implementation or two... thanks, --titus -- C. Titus Brown, c...@msu.edu --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "pygr-dev" group. To post to this group, send email to pygr-dev@googlegroups.com To unsubscribe from this group, send email to pygr-dev+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/pygr-dev?hl=en -~----------~----~----~----~------~----~------~--~---
