def setup_supermatrix(self):
"""
Sets up supermatrix for some tests
"""
from supermatrix import Supermatrix, Otu
# make taxa
alpha = Otu("alpha")
beta = Otu("beta")
pi = Otu("pi")
omega = Otu("omega")
gamma = Otu("gamma")
# add sequence data to taxa, all that matters is the sequence length
alpha_seq_lengths = [10, 0, 10, 0]
beta_seq_lengths = [5, 10, 0, 0]
pi_seq_lengths = [8, 6, 0, 4]
omega_seq_lengths = [0, 0, 8, 9]
gamma_seq_lengths = [0, 10, 0, 0]
for length in alpha_seq_lengths:
alpha.update("-", "x", length)
for length in beta_seq_lengths:
beta.update("-", "x", length)
for length in pi_seq_lengths:
pi.update("-", "x", length)
for length in omega_seq_lengths:
omega.update("-", "x", length)
for length in gamma_seq_lengths:
gamma.update("-", "x", length)
sm = Supermatrix()
sm.otus = {"alpha": alpha, "beta": beta, "pi": pi, "omega": omega, "gamma": gamma}
sm.get_PD()
return sm
