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_forward():
k = 4
n = 1e4
rho = 1.5e-8 * 20
mu = 2.5e-8 * 20
length = int(100e3 / 20)
times = argweaver.get_time_points(ntimes=100)
arg = arglib.sample_arg_smc(k, 2 * n, rho, start=0, end=length)
muts = arglib.sample_arg_mutations(arg, mu)
seqs = arglib.make_alignment(arg, muts)
print "muts", len(muts)
print "recomb", len(arglib.get_recomb_pos(arg))
argweaver.discretize_arg(arg, times)
# remove chrom
new_name = "n%d" % (k - 1)
arg = argweaver.remove_arg_thread(arg, new_name)
carg = argweaverc.arg2ctrees(arg, times)
util.tic("C fast")
probs1 = argweaverc.argweaver_forward_algorithm(carg, seqs, times=times)
util.toc()
util.tic("C slow")
probs2 = argweaverc.argweaver_forward_algorithm(carg,
seqs,
times=times,
slow=True)
util.toc()
for i, (col1, col2) in enumerate(izip(probs1, probs2)):
for a, b in izip(col1, col2):
fequal(a, b, rel=.0001)
def test_forward():
k = 4
n = 1e4
rho = 1.5e-8 * 20
mu = 2.5e-8 * 20
length = int(100e3 / 20)
times = argweaver.get_time_points(ntimes=100)
arg = arglib.sample_arg_smc(k, 2*n, rho, start=0, end=length)
muts = arglib.sample_arg_mutations(arg, mu)
seqs = arglib.make_alignment(arg, muts)
print "muts", len(muts)
print "recomb", len(arglib.get_recombs(arg))
argweaver.discretize_arg(arg, times)
# remove chrom
new_name = "n%d" % (k - 1)
arg = argweaver.remove_arg_thread(arg, new_name)
carg = argweaverc.arg2ctrees(arg, times)
util.tic("C fast")
probs1 = argweaverc.argweaver_forward_algorithm(carg, seqs, times=times)
util.toc()
util.tic("C slow")
probs2 = argweaverc.argweaver_forward_algorithm(carg, seqs, times=times,
slow=True)
util.toc()
for i, (col1, col2) in enumerate(izip(probs1, probs2)):
for a, b in izip(col1, col2):
fequal(a, b, rel=.0001)