def mutate(parent_seq, model, time):
nucs = ('A','C','G','T')
new_seq = []
for parent_nuc in parent_seq:
probs = []
for child_nuc in nucs:
probs.append(model.matrix[parent_nuc][child_nuc](time))
# print probs
new_nuc = four_category_dist(1, probs, nucs)[0]
new_seq.append(new_nuc)
return new_seq
def select_sequence(self, target, topo, t):
nucs = ("A", "T", "C", "G")
freqs = {"A": 0.0, "T": 0.0, "C": 0.0, "G": 0.0}
new_seq = []
parent = target.parent
for seq in self.target.sequence:
for nuc in nucs:
p = self.model.matrix[seq][nuc](parent.time - t)
c1 = self.model.matrix[nuc][seq](t - topo[1].time)
c2 = self.model.matrix[nuc][seq](t - topo[2].time)
freqs[nuc] += (p * c1 * c2) / 4
new_nuc = four_category_dist(1, freqs.values(), nucs)[0]
new_seq.append(new_nuc)
return new_seq
