def test_gtr(self):
kappa = 6.122449
m = RevDiscStateContTimeModel(state_freq=(0.3, 0.25, 0.2, 0.25),
r_upper=[[1.0, kappa, 1.0 ],
[ 1.0, kappa ],
[ 1.0 ]]
)
assert_list_of_mat_eq(self, m.prob_matrices(0.01), [[[0.991443333333, 0.001247, 0.00606333333333, 0.001247, ],
[0.0014964, 0.989928, 0.0009976, 0.007576],
[0.009095, 0.001247, 0.988415, 0.001247],
[0.0014964, 0.007576, 0.0009976, 0.989928]]])
invoc = '%s %s %s >%s 2>%s' % (os.path.join(d, 'src', 'PhyPatClassProb'), opts, fn, stdo, stde)
sys.stderr.write('Creating/Overwriting %s and %s by running:\n %s\n' % (stdo, stde, invoc))
rc = os.system(invoc)
if rc != 0:
sys.stderr.write('Error! return code = %d\n' % rc)
sys.exit(0)
################################################################################
# call beagle in phython
################################################################################
from pytbeaglehon.disc_state_cont_time_model import RevDiscStateContTimeModel
m = RevDiscStateContTimeModel(state_freq=state_freq,
r_upper=[[rAC, rAG, rAT ],
[ rCG, rCT ],
[ rGT ]])
p_mat = m.prob_matrices(edge_length)
################################################################################
################################################################################
# Format output
################################################################################
p_mat_str = [[str(i) for i in row] for row in p_mat[0]]
max_str_len = max([max([len(i) for i in row]) for row in p_mat_str])
p_mat_str = [[i.ljust(max_str_len) for i in row] for row in p_mat_str]
for row in p_mat_str:
print '\t'.join(row)
################################################################################
# Produce optional output
elif arg == '-e':
if read_edge_len:
sys.exit("Expected only one -e per invocation")
curr_list = []
reading_edge_len = True
if reading_freq:
sys.exit("Expected 3 base frequencies")
elif reading_rmat:
sys.exit("Expected 5 relative rate parameters")
elif reading_edge_len:
sys.exit("Expected an edge length parameter")
# Arguments have been parsed. Do the calculation...
model = RevDiscStateContTimeModel(state_freq=freq, r_upper=r_mat)
mat = model.calc_prob_matrices(edge_length)[0] # returns a list of matrices, but we are not
# using rate het, so we just want
# the first.
# format the output
max_len = 0
mat_str = [list(' ACGT')]
for from_base, mat_row in izip('ACGT', mat):
mat_str_row = [from_base]
for cell in mat_row:
s = str(cell)
if len(s) > max_len:
max_len = len(s)
