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 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)
#arg = arglib.read_arg("tmp/a.arg")
#arg.set_ancestral()
#find_recomb_coal(tree, last_tree, recomb_name=None, pos=None)
times = arghmm.get_time_points(30, maxtime=60e3)
arghmm.discretize_arg(arg, times)
# get recombs
recombs = list(x.pos for x in arghmm.iter_visible_recombs(arg))
print "recomb", recombs
pos = recombs[0] + 1
tree = arg.get_marginal_tree(pos-.5)
last_tree = arg.get_marginal_tree(pos-1-.5)
r, c = arghmm.find_recomb_coal(tree, last_tree, pos=pos)
#treelib.draw_tree_names(last_tree.get_tree(), minlen=5, maxlen=5)
#treelib.draw_tree_names(tree.get_tree(), minlen=5, maxlen=5)
model = arghmm.ArgHmm(arg, seqs, new_name="n%d" % (k-1), times=times)
#================================================================
win = summon.Window()
layout = argvis.layout_arg(last_tree)
win.add_group(argvis.draw_arg(last_tree, layout))
layout2 = argvis.layout_arg(tree)
for node, (x,y) in layout2.items():
#arg = arglib.read_arg("tmp/a.arg")
#arg.set_ancestral()
#find_recomb_coal(tree, last_tree, recomb_name=None, pos=None)
times = arghmm.get_time_points(30, maxtime=60e3)
arghmm.discretize_arg(arg, times)
# get recombs
recombs = list(x.pos for x in arghmm.iter_visible_recombs(arg))
print "recomb", recombs
pos = recombs[0] + 1
tree = arg.get_marginal_tree(pos - .5)
last_tree = arg.get_marginal_tree(pos - 1 - .5)
r, c = arghmm.find_recomb_coal(tree, last_tree, pos=pos)
#treelib.draw_tree_names(last_tree.get_tree(), minlen=5, maxlen=5)
#treelib.draw_tree_names(tree.get_tree(), minlen=5, maxlen=5)
model = arghmm.ArgHmm(arg, seqs, new_name="n%d" % (k - 1), times=times)
#================================================================
win = summon.Window()
layout = argvis.layout_arg(last_tree)
win.add_group(argvis.draw_arg(last_tree, layout))
layout2 = argvis.layout_arg(tree)
for node, (x, y) in layout2.items():
layout2[node] = (x + 20, y)
def test_determ(self):
k = 8
n = 1e4
rho = 1.5e-8
mu = 2.5e-8
length = 100000
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(maxtime=50000, ntimes=20)
arghmm.discretize_arg(arg, times)
new_name = "n%d" % (k - 1)
thread = list(
arghmm.iter_chrom_thread(arg, arg[new_name], by_block=False))
thread_clades = list(
arghmm.iter_chrom_thread(arg,
arg[new_name],
by_block=True,
use_clades=True))
# remove chrom
keep = ["n%d" % i for i in range(k - 1)]
arglib.subarg_by_leaf_names(arg, keep)
arg = arglib.smcify_arg(arg)
model = arghmm.ArgHmm(arg,
seqs,
new_name=new_name,
times=times,
rho=rho,
mu=mu)
for i, rpos in enumerate(model.recomb_pos[1:-1]):
pos = rpos + 1
model.check_local_tree(pos, force=True)
#recomb = arghmm.find_tree_next_recomb(arg, pos - 1)
tree = arg.get_marginal_tree(pos - .5)
last_tree = arg.get_marginal_tree(pos - 1 - .5)
states1 = model.states[pos - 1]
states2 = model.states[pos]
(recomb_branch, recomb_time), (coal_branch, coal_time) = \
arghmm.find_recomb_coal(tree, last_tree, pos=rpos)
recomb_time = times.index(recomb_time)
coal_time = times.index(coal_time)
determ = arghmm.get_deterministic_transitions(
states1, states2, times, tree, last_tree, recomb_branch,
recomb_time, coal_branch, coal_time)
leaves1, time1, block1 = thread_clades[i]
leaves2, time2, block2 = thread_clades[i + 1]
if new_name in leaves1:
leaves1.remove(new_name)
if new_name in leaves2:
leaves2.remove(new_name)
node1 = arghmm.arg_lca(arg, leaves1, None, pos - 1).name
node2 = arghmm.arg_lca(arg, leaves2, None, pos).name
state1 = (node1, times.index(time1))
state2 = (node2, times.index(time2))
print pos, state1, state2
try:
statei1 = states1.index(state1)
statei2 = states2.index(state2)
except:
print "states1", states1
print "states2", states2
raise
statei3 = determ[statei1]
print " ", statei1, statei2, statei3, states2[statei3]
if statei2 != statei3 and statei3 != -1:
tree = tree.get_tree()
treelib.remove_single_children(tree)
last_tree = last_tree.get_tree()
treelib.remove_single_children(last_tree)
print "block1", block1
print "block2", block2
print "r=", (recomb_branch, recomb_time)
print "c=", (coal_branch, coal_time)
print "tree"
treelib.draw_tree_names(tree, minlen=8, maxlen=8)
print "last_tree"
treelib.draw_tree_names(last_tree, minlen=8, maxlen=8)
assert False
def test_determ(self):
k = 8
n = 1e4
rho = 1.5e-8
mu = 2.5e-8
length = 100000
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(maxtime=50000, ntimes=20)
arghmm.discretize_arg(arg, times)
new_name = "n%d" % (k - 1)
thread = list(arghmm.iter_chrom_thread(arg, arg[new_name],
by_block=False))
thread_clades = list(arghmm.iter_chrom_thread(
arg, arg[new_name], by_block=True, use_clades=True))
# remove chrom
keep = ["n%d" % i for i in range(k-1)]
arglib.subarg_by_leaf_names(arg, keep)
arg = arglib.smcify_arg(arg)
model = arghmm.ArgHmm(arg, seqs, new_name=new_name, times=times,
rho=rho, mu=mu)
for i, rpos in enumerate(model.recomb_pos[1:-1]):
pos = rpos + 1
model.check_local_tree(pos, force=True)
#recomb = arghmm.find_tree_next_recomb(arg, pos - 1)
tree = arg.get_marginal_tree(pos-.5)
last_tree = arg.get_marginal_tree(pos-1-.5)
states1 = model.states[pos-1]
states2 = model.states[pos]
(recomb_branch, recomb_time), (coal_branch, coal_time) = \
arghmm.find_recomb_coal(tree, last_tree, pos=rpos)
recomb_time = times.index(recomb_time)
coal_time = times.index(coal_time)
determ = arghmm.get_deterministic_transitions(
states1, states2, times,
tree, last_tree,
recomb_branch, recomb_time,
coal_branch, coal_time)
leaves1, time1, block1 = thread_clades[i]
leaves2, time2, block2 = thread_clades[i+1]
if new_name in leaves1:
leaves1.remove(new_name)
if new_name in leaves2:
leaves2.remove(new_name)
node1 = arghmm.arg_lca(arg, leaves1, None, pos-1).name
node2 = arghmm.arg_lca(arg, leaves2, None, pos).name
state1 = (node1, times.index(time1))
state2 = (node2, times.index(time2))
print pos, state1, state2
try:
statei1 = states1.index(state1)
statei2 = states2.index(state2)
except:
print "states1", states1
print "states2", states2
raise
statei3 = determ[statei1]
print " ", statei1, statei2, statei3, states2[statei3]
if statei2 != statei3 and statei3 != -1:
tree = tree.get_tree()
treelib.remove_single_children(tree)
last_tree = last_tree.get_tree()
treelib.remove_single_children(last_tree)
print "block1", block1
print "block2", block2
print "r=", (recomb_branch, recomb_time)
print "c=", (coal_branch, coal_time)
print "tree"
treelib.draw_tree_names(tree, minlen=8, maxlen=8)
print "last_tree"
treelib.draw_tree_names(last_tree, minlen=8, maxlen=8)
assert False