def get_mapping(tree1, tree2, pos, times):
recomb, coal = arghmm.find_recomb_coal(tree2, tree1, pos=pos)
states1 = list(arghmm.iter_coal_states(tree1, times))
states2 = list(arghmm.iter_coal_states(tree2, times))
for i, (node1, time1) in enumerate(states1):
j = arghmm.get_deterministic_transition(
(node1, time1), states2, times, tree2, tree1,
recomb[0], times.index(recomb[1]),
coal[0], times.index(coal[1]))
node2, time2 = states2[j]
yield (node1, time1), (node2, time2)
def test_nlineages(self):
"""
Test lineage counting
"""
k = 4
n = 1e4
rho = 1.5e-8 * 1
length = 1000
arg = arglib.sample_arg(k, n, rho, start=0, end=length)
times = arghmm.get_time_points(ntimes=6)
arghmm.discretize_arg(arg, times)
tree = arg.get_marginal_tree(0)
nlineages, nrecombs, ncoals = arghmm.get_nlineages_recomb_coal(
tree, times)
treelib.draw_tree_names(tree.get_tree(), scale=4e-3)
print list(arghmm.iter_coal_states(tree, times))
print nlineages
self.assert_(nlineages == sorted(nlineages, reverse=True))
print nlineages
print nrecombs
print ncoals
def test_states(self):
"""
Test state enumeration
"""
k = 2
n = 1e4
rho = 1.5e-8 * 100
length = 1000
for i in xrange(20):
arg = arglib.sample_arg(k, n, rho, start=0, end=length)
times = arghmm.get_time_points(10)
arghmm.discretize_arg(arg, times)
tree = arg.get_marginal_tree(0)
states = list(arghmm.iter_coal_states(tree, times))
treelib.draw_tree_names(tree.get_tree(), scale=4e-4,
minlen=6, maxlen=6)
print states
def test_states(self):
"""
Test state enumeration
"""
k = 2
n = 1e4
rho = 1.5e-8 * 100
length = 1000
for i in range(20):
arg = arglib.sample_arg(k, n, rho, start=0, end=length)
times = arghmm.get_time_points(10)
arghmm.discretize_arg(arg, times)
tree = arg.get_marginal_tree(0)
states = list(arghmm.iter_coal_states(tree, times))
treelib.draw_tree_names(tree.get_tree(),
scale=4e-4,
minlen=6,
maxlen=6)
print(states)
