def Edge(seq1, seq2, length, bin_data, switch=1.0, bprobs=None):
# one sequence pair in, potentialy, a tree
bins = len(bin_data)
pair = pairwise.Pair(seq1, seq2)
EP = pair.makeReversibleEmissionProbs([(bin.mprobs, bin.Qd) for bin in bin_data], length)
tms = [bin.indel.calcTransitionMatrix(length) for bin in bin_data]
if bins == 1:
TM = tms[0]
else:
assert bprobs
R = SiteClassTransitionMatrix(switch, bprobs)
TM = R.nestTransitionMatricies(tms)
assert min(TM.Matrix.flat) >=0, bin_data
return EP.makePairHMM(TM)
def Edge(seq1, seq2, length, bin_data, switch=1.0, bprobs=None):
# one sequence pair in, potentialy, a tree
bins = len(bin_data)
pair = pairwise.Pair(seq1, seq2)
EP = pair.makeReversibleEmissionProbs([(bin.mprobs, bin.Qd) for bin in bin_data], length)
tms = [bin.indel.calcTransitionMatrix(length) for bin in bin_data]
if bins == 1:
TM = tms[0]
else:
assert bprobs
R = SiteClassTransitionMatrix(switch, bprobs)
TM = R.nestTransitionMatricies(tms)
assert min(TM.Matrix.flat) >=0, bin_data
return EP.makePairHMM(TM)
