Hi all,
I've made some progress on the seq_frame branch, which adds
a 'translation' method to DNA sequences; for example, you can do
frame1 = dna_seq.translation(1)
frame2 = dna_seq.translation(2)
frame3 = dna_seq.translation(3)
to get the three-frame translation of dna_seq.
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.
Does anyone have thoughts on this? It's OK to say "I have no idea what
you're talking about", too ;). I find silence ominous...
You can check it out from git://github.com/ctb/pygr.git, branch
'seq_frame'. Comments welcome.
thanks,
--titus
--
C. Titus Brown, [email protected]
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