def test_emit_internal():
"""
Calculate emission probabilities for internal branches
"""
k = 10
n = 1e4
rho = 1.5e-8 * 20
mu = 2.5e-8 * 20
length = int(10e3) / 20
times = argweaver.get_time_points(ntimes=20, maxtime=200000)
arg = argweaver.sample_arg_dsmc(k,
2 * n,
rho,
start=0,
end=length,
times=times)
muts = argweaver.sample_arg_mutations(arg, mu, times)
seqs = argweaver.make_alignment(arg, muts)
trees, names = argweaverc.arg2ctrees(arg, times)
seqs2, nseqs, seqlen = argweaverc.seqs2cseqs(seqs, names)
assert argweaverc.argweaver_assert_emit_internal(trees, len(times), times,
mu, seqs2, nseqs, seqlen)
def test_emit():
"""
Calculate emission probabilities
"""
k = 10
n = 1e4
rho = 1.5e-8 * 20
mu = 2.5e-8 * 20
length = int(1e3) / 20
times = argweaver.get_time_points(ntimes=20, maxtime=200000)
arg = argweaver.sample_arg_dsmc(k,
2 * n,
rho,
start=0,
end=length,
times=times)
muts = argweaver.sample_arg_mutations(arg, mu, times)
seqs = argweaver.make_alignment(arg, muts)
new_name = "n%d" % (k - 1)
arg = argweaver.remove_arg_thread(arg, new_name)
trees, names = argweaverc.arg2ctrees(arg, times)
seqs2, nseqs, seqlen = argweaverc.seqs2cseqs(seqs, names + [new_name])
assert argweaverc.argweaver_assert_emit(trees, len(times), times, mu,
seqs2, nseqs, seqlen)
def test_emit():
"""
Calculate emission probabilities
"""
k = 10
n = 1e4
rho = 1.5e-8 * 20
mu = 2.5e-8 * 20
length = int(1e3) / 20
times = argweaver.get_time_points(ntimes=20, maxtime=200000)
arg = argweaver.sample_arg_dsmc(k, 2*n, rho, start=0, end=length,
times=times)
muts = argweaver.sample_arg_mutations(arg, mu, times)
seqs = argweaver.make_alignment(arg, muts)
new_name = "n%d" % (k-1)
arg = argweaver.remove_arg_thread(arg, new_name)
trees, names = argweaverc.arg2ctrees(arg, times)
seqs2, nseqs, seqlen = argweaverc.seqs2cseqs(seqs, names + [new_name])
assert argweaverc.argweaver_assert_emit(trees, len(times), times, mu,
seqs2, nseqs, seqlen)
def test_arg_joint():
"""
Compute joint probability of an ARG
"""
k = 2
n = 1e4
rho = 1.5e-8 * 20
mu = 2.5e-8 * 20
length = 10000
times = argweaver.get_time_points(ntimes=20, maxtime=200000)
arg = argweaver.sample_arg_dsmc(k, 2*n, rho, start=0, end=length,
times=times)
muts = argweaver.sample_arg_mutations(arg, mu, times=times)
seqs = arglib.make_alignment(arg, muts)
lk = argweaver.calc_joint_prob(arg, seqs, mu=mu, rho=rho, times=times)
print lk
def test_emit_internal():
"""
Calculate emission probabilities for internal branches
"""
k = 10
n = 1e4
rho = 1.5e-8 * 20
mu = 2.5e-8 * 20
length = int(10e3) / 20
times = argweaver.get_time_points(ntimes=20, maxtime=200000)
arg = argweaver.sample_arg_dsmc(k, 2*n, rho, start=0, end=length,
times=times)
muts = argweaver.sample_arg_mutations(arg, mu, times)
seqs = argweaver.make_alignment(arg, muts)
trees, names = argweaverc.arg2ctrees(arg, times)
seqs2, nseqs, seqlen = argweaverc.seqs2cseqs(seqs, names)
assert argweaverc.argweaver_assert_emit_internal(
trees, len(times), times, mu, seqs2, nseqs, seqlen)