def test_bw_beta_all_equal(self):
# check that all betas are the same
# get_beta() function already implemented in hmm.py as part of the
# support code
beta = get_beta(self.seq, self.model)
print "beta: "
format_array_print(beta)
num_rows = shape(beta)[0]
num_cols = shape(beta)[1]
for r in range(num_rows):
for c in range(num_cols):
self.assertAlmostEqual(beta[r, c], 1.0 / 3)
def test_bw_gamma_first_col_equal(self):
# check that the first column of gamma are the same
# get_gamma(), get_beta(), get_alpha() functions already implemented in
# hmm.py as part of the support code
alpha, logp = get_alpha(self.seq, self.model)
beta = get_beta(self.seq, self.model)
gamma = get_gamma(alpha, beta)
print "gamma: "
format_array_print(gamma)
gamma_first_value = gamma[0, 0]
num_rows = shape(gamma)[0]
for r in range(1, num_rows):
self.assertAlmostEqual(gamma_first_value, gamma[r, 0])
