Python GammaMixture.update_transition_matrix Examples

Example #1

File: test.py Project: kgori/phylo_utils

print gamma.get_sitewise_likelihoods()

kappa = 2
k80 = K80(kappa)
tm = TransitionMatrix(k80)

partials_dict = {
    "1": seq_to_partials("ACCCT"),
    "2": seq_to_partials("TCCCT"),
    "3": seq_to_partials("TCGGT"),
    "4": seq_to_partials("ACCCA"),
    "5": seq_to_partials("CCCCC"),
}

gamma = GammaMixture(0.03, 4)
gamma.init_models(tm, partials_dict, scale_freq=200)
gamma.set_tree(t)
print gamma.get_likelihood()
print gamma.get_sitewise_likelihoods()
print gamma.get_sitewise_likelihoods().sum(0)

gamma.update_alpha(1.0)
print gamma.get_likelihood()
print gamma.get_sitewise_likelihoods()
print gamma.get_sitewise_likelihoods().sum(0)

gamma.update_transition_matrix(TransitionMatrix(K80(3)))
print gamma.get_likelihood()
print gamma.get_sitewise_likelihoods()
print gamma.get_sitewise_likelihoods().sum(0)