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)
mat_str_row.append(s)
