On Thu, Jul 16, 2009 at 06:20:14PM -0700, Christopher Lee wrote: -> On Jun 28, 2009, at 4:41 PM, C. Titus Brown wrote: -> -> > I've finished the positive-frame translation code & tests, as of the -> > latest commit; see sequence_test.py. The math was tricky ;). The -> > only -> > complication I've run into is that the returned amino acid sequence -> > object (which is an Annotation, really) always returns the frame of -> > its -> > full-length parent amino acid translation. For example, in this code: -> > -> > x = s[1:4].translation(1) # frame 1 @ nt 1 -> > y = s.translation(2)[:1] # == frame 2, aa 0 -> > assert str(x) == str(y) -> > assert y.frame == 2 -> > -> > 'x.frame' here is 2, rather than 1, because it's a translation in -> > frame -> > 1 of a slice starting at position 1, hence equal to frame 2... I did -> > think of a way to get the frame to properly reflect the frame relative -> > to the DNA slice, but it's ugly and potentially leaky, and I haven't -> > decided if it's a good idea. -> -> Hi Titus, -> to me this seems like a question of definition: what does "frame" -> mean? Personally, I think we should keep it simple by defining frame -> strictly in terms of the top-level sequence (it's too confusing to -> start talking about "frame-relative-to-this", "frame-relative-to-that" -> etc.). The frame property that you introduced some time ago defines -> it in that simple way, which seems fine by me. -> -> People who want to calculate "relative frame" can do so trivially -> (it's just addition / subtraction of the absolute frames mod 3).
I agree with the decision although the math for negative frames seemed more complicated... cheers, --t -- 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 -~----------~----~----~----~------~----~------~--~---
