def __init__(self, switch, bprobs):
half = len(bprobs) // 2
self.alloc = [0] * half + [1] * (len(bprobs) - half)
pprobs = numpy.zeros([max(self.alloc) + 1], Float)
for (b, p) in zip(self.alloc, bprobs):
pprobs[b] += p
self.bprobs = [
p / pprobs[self.alloc[i]] for (i, p) in enumerate(bprobs)
]
self.transition_matrix = SiteClassTransitionMatrix(switch, pprobs)
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)
