On Jul 17, 2009, at 11:15 AM, C. Titus Brown wrote: > "Position mod 3" does work for forward frames. For RC frames, it > may be > as simple as doing a transform -- I think that -1 -> - (+1), while > -2 -> > -(+3) and -3 -> -(+2).
A big simplification in Pygr is that all coordinates (negative as well as positive) are given relative to the start of the positive coordinate system, i.e. -(seq[10:50]) == (-seq)[-50:-10] the coordinates for the first interval are (10,50) and for the second (-50,-10) TranslationDB calculates the positive frame as abs(start) % 3. If start<0 then the frame is negative. Thus frame "-0" is just the translation of the reverse complement of frame "0". Rather than thinking of this as "-0", think of this as two separate variables, one specifying the frame (0, 1, 2) and the other specifying the strand (+ or -). -- 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 -~----------~----~----~----~------~----~------~--~---
