def do_mut_path_3_end(fs, to_gtr):
out = StringIO()
# define the path mutation rate matrix
M = mrate.get_path_rate_matrix(3)
print >> out, '*** mutation rate matrix (3-state path) ***'
print >> out
print >> out, get_rate_matrix_summary(M)
print >> out
print >> out
# kill the middle state by natural selection
p_target = ((1 - fs.p_mid)/2, (1 - fs.p_mid)/2, fs.p_mid)
Q = to_gtr(M, p_target)
print >> out, '*** mutation-selection balance ***'
print >> out
print >> out, get_rate_matrix_summary(Q)
print >> out
print >> out
# define a reference mutation rate matrix that is a scaled schur complement
M = mrate.get_path_rate_matrix(2)
print >> out, '*** reference mutation rate matrix (2-state path) ***'
print >> out
print >> out, get_rate_matrix_summary(M)
print >> out
print >> out
return out.getvalue().rstrip()
def do_mut_complete_3(fs, to_gtr):
out = StringIO()
# define the path mutation rate matrix
M = mrate.get_dense_sequence_rate_matrix(3, 1)
print >> out, '*** mutation rate matrix (3-state complete) ***'
print >> out
print >> out, get_rate_matrix_summary(M)
print >> out
print >> out
# kill the middle state by natural selection
p_other = (1 - fs.p_mid)/2
p_target = (p_other, p_other, fs.p_mid)
Q = to_gtr(M, p_target)
print >> out, '*** mutation-selection balance ***'
print >> out
print >> out, get_rate_matrix_summary(Q)
print >> out
print >> out
# define a reference mutation rate matrix
M = mrate.get_path_rate_matrix(2)
print >> out, '*** reference mutation rate matrix (2-state path) ***'
print >> out
print >> out, get_rate_matrix_summary(M)
print >> out
print >> out
return out.getvalue().rstrip()
def do_mut_hyper_2_2(fs, to_gtr):
out = StringIO()
# define the path mutation rate matrix
M = mrate.get_sparse_sequence_rate_matrix(2, 2)
print >> out, '*** mutation rate matrix (4-state square) ***'
print >> out
print >> out, get_rate_matrix_summary(M)
print >> out
print >> out
# kill the last state by natural selection
p_other = (1 - fs.p_mid)/3
p_target = (p_other, p_other, p_other, fs.p_mid)
Q = to_gtr(M, p_target)
print >> out, '*** mutation-selection balance ***'
print >> out
print >> out, get_rate_matrix_summary(Q)
print >> out
print >> out
# define a reference mutation rate matrix
M = mrate.get_path_rate_matrix(3)
print >> out, '*** reference mutation rate matrix (3-state path) ***'
print >> out
print >> out, get_rate_matrix_summary(M)
print >> out
print >> out
return out.getvalue().rstrip()
def do_mut_path_2(fs, to_gtr):
out = StringIO()
# define the path mutation rate matrix
M = mrate.get_path_rate_matrix(2)
print >> out, '*** mutation rate matrix (2-state path) ***'
print >> out
print >> out, get_rate_matrix_summary(M)
print >> out
print >> out
# kill the last state by natural selection
p_target = ((1 - fs.p_mid), fs.p_mid)
Q = to_gtr(M, p_target)
print >> out, '*** mutation-selection balance ***'
print >> out
print >> out, get_rate_matrix_summary(Q)
print >> out
print >> out
return out.getvalue().rstrip()
