def test_backward_c(self):
k = 3
n = 1e4
rho = 1.5e-8 * 30
mu = 2.5e-8 * 100
length = 100
arg = arglib.sample_arg(k, n, rho, start=0, end=length)
arg.prune()
muts = arglib.sample_arg_mutations(arg, mu)
seqs = arglib.make_alignment(arg, muts)
print arglib.get_recomb_pos(arg)
print "muts", len(muts)
print "recomb", len(arglib.get_recomb_pos(arg))
times = arghmm.get_time_points(ntimes=10)
arghmm.discretize_arg(arg, times)
tree = arg.get_marginal_tree(0)
print tree.root.age
treelib.draw_tree_names(tree.get_tree(), minlen=5, scale=4e-4)
# remove chrom
keep = ["n%d" % i for i in range(k - 1)]
arglib.subarg_by_leaf_names(arg, keep)
model = arghmm.ArgHmm(arg,
seqs,
new_name="n%d" % (k - 1),
times=times,
rho=rho,
mu=mu)
print "states", len(model.states[0])
util.tic("C")
probs1 = list(arghmm.backward_algorithm(model, length, verbose=True))
util.toc()
util.tic("python")
probs2 = list(hmm.backward_algorithm(model, length, verbose=True))
util.toc()
print "probs1"
pc(probs1)
print "probs2"
pc(probs2)
for col1, col2 in izip(probs1, probs2):
for a, b in izip(col1, col2):
fequal(a, b)
def test_backward_c(self):
k = 3
n = 1e4
rho = 1.5e-8 * 30
mu = 2.5e-8 * 100
length = 100
arg = arglib.sample_arg(k, n, rho, start=0, end=length)
arg.prune()
muts = arglib.sample_arg_mutations(arg, mu)
seqs = arglib.make_alignment(arg, muts)
print arglib.get_recomb_pos(arg)
print "muts", len(muts)
print "recomb", len(arglib.get_recomb_pos(arg))
times = arghmm.get_time_points(ntimes=10)
arghmm.discretize_arg(arg, times)
tree = arg.get_marginal_tree(0)
print tree.root.age
treelib.draw_tree_names(tree.get_tree(), minlen=5, scale=4e-4)
# remove chrom
keep = ["n%d" % i for i in range(k-1)]
arglib.subarg_by_leaf_names(arg, keep)
model = arghmm.ArgHmm(arg, seqs, new_name="n%d" % (k-1), times=times,
rho=rho, mu=mu)
print "states", len(model.states[0])
util.tic("C")
probs1 = list(arghmm.backward_algorithm(model, length, verbose=True))
util.toc()
util.tic("python")
probs2 = list(hmm.backward_algorithm(model, length, verbose=True))
util.toc()
print "probs1"
pc(probs1)
print "probs2"
pc(probs2)
for col1, col2 in izip(probs1, probs2):
for a, b in izip(col1, col2):
fequal(a, b)
def test_backward(self):
"""
Run backward algorithm
"""
k = 3
n = 1e4
rho = 1.5e-8 * 100
mu = 2.5e-8 * 100
length = 10000
arg = arglib.sample_arg(k, n, rho, start=0, end=length)
muts = arglib.sample_arg_mutations(arg, mu)
seqs = arglib.make_alignment(arg, muts)
times = arghmm.get_time_points(ntimes=10)
arghmm.discretize_arg(arg, times)
tree = arg.get_marginal_tree(0)
print tree.root.age
treelib.draw_tree_names(tree.get_tree(), minlen=5, scale=4e-4)
# remove chrom
new_name = "n%d" % (k - 1)
arg = arghmm.remove_arg_thread(arg, new_name)
model = arghmm.ArgHmm(arg,
seqs,
new_name=new_name,
times=times,
rho=rho,
mu=mu)
print "states", len(model.states[0])
print "recomb", model.recomb_pos
print "muts", len(muts)
probs = hmm.backward_algorithm(model, length, verbose=True)
for pcol in probs:
p = sum(map(exp, pcol))
print p, " ".join("%.3f" % f for f in map(exp, pcol))
def test_backward(self):
"""
Run backward algorithm
"""
k = 3
n = 1e4
rho = 1.5e-8 * 100
mu = 2.5e-8 * 100
length = 10000
arg = arglib.sample_arg(k, n, rho, start=0, end=length)
muts = arglib.sample_arg_mutations(arg, mu)
seqs = arglib.make_alignment(arg, muts)
times = arghmm.get_time_points(ntimes=10)
arghmm.discretize_arg(arg, times)
tree = arg.get_marginal_tree(0)
print tree.root.age
treelib.draw_tree_names(tree.get_tree(), minlen=5, scale=4e-4)
# remove chrom
new_name = "n%d" % (k-1)
arg = arghmm.remove_arg_thread(arg, new_name)
model = arghmm.ArgHmm(arg, seqs, new_name=new_name, times=times,
rho=rho, mu=mu)
print "states", len(model.states[0])
print "recomb", model.recomb_pos
print "muts", len(muts)
probs = hmm.backward_algorithm(model, length, verbose=True)
for pcol in probs:
p = sum(map(exp, pcol))
print p, " ".join("%.3f" % f for f in map(exp, pcol))