def test_iter_sprs_time(self):
rho = 1.5e-8 # recomb/site/gen
l = 100000 # length of locus
k = 40 # number of lineages
n = 2*10000 # effective popsize
arg = arglib.sample_arg(k, n, rho, 0, l)
x = list(arglib.iter_arg_sprs(arg))
x = list(arglib.iter_arg_sprs_simple(arg))
x = list(arglib.iter_arg_sprs(arg, use_leaves=True))
x = list(arglib.iter_arg_sprs_simple(arg, use_leaves=True))
x
def test_trans_switch():
"""
Calculate transition probabilities for switch matrix
Only calculate a single matrix
"""
k = 12
n = 1e4
rho = 1.5e-8 * 20
length = 1000
times = argweaver.get_time_points(ntimes=20, maxtime=200000)
popsizes = [n] * len(times)
recombs = []
while len(recombs) == 0:
arg = argweaver.sample_arg_dsmc(k,
2 * n,
rho,
start=0,
end=length,
times=times)
recombs = [x.pos for x in arg if x.event == "recomb"]
pos = recombs[0]
tree = arg.get_marginal_tree(pos - .5)
rpos, r, c = arglib.iter_arg_sprs(arg, start=pos - .5).next()
spr = (r, c)
assert argweaverc.assert_transition_switch_probs(tree, spr, times,
popsizes, rho)
def test_trans_switch(self):
"""
Calculate transition probabilities for k=2
Only calculate a single matrix
"""
k = 12
n = 1e4
rho = 1.5e-8 * 20
mu = 2.5e-8 * 20
length = 1000
times = arghmm.get_time_points(ntimes=20, maxtime=200000)
popsizes = [n] * len(times)
recombs = []
while len(recombs) == 0:
arg = arghmm.sample_arg_dsmc(k, 2*n, rho, start=0, end=length,
times=times)
recombs = [x.pos for x in arg if x.event == "recomb"]
pos = recombs[0]
tree = arg.get_marginal_tree(pos-.5)
rpos, r, c = arglib.iter_arg_sprs(arg, start=pos-.5).next()
spr = (r, c)
assert arghmm.assert_transition_switch_probs(tree, spr,
times, popsizes, rho)
def test_arg_equal(arg, arg2):
# test recomb points
recombs = sorted(x.pos for x in arg if x.event == "recomb")
recombs2 = sorted(x.pos for x in arg2 if x.event == "recomb")
assert recombs == recombs2
# check local tree topologies
for (start, end), tree in arglib.iter_tree_tracks(arg):
pos = (start + end) / 2.0
arglib.remove_single_lineages(tree)
tree1 = tree.get_tree()
tree2 = arg2.get_marginal_tree(pos)
arglib.remove_single_lineages(tree2)
tree2 = tree2.get_tree()
hash1 = phylo.hash_tree(tree1)
hash2 = phylo.hash_tree(tree2)
print
print pos
print hash1
print hash2
assert hash1 == hash2
# check sprs
sprs1 = arglib.iter_arg_sprs(arg, use_leaves=True)
sprs2 = arglib.iter_arg_sprs(arg2, use_leaves=True)
for (pos1, recomb1, coal1), (pos2, recomb2, coal2) in izip(sprs1, sprs2):
recomb1 = (sorted(recomb1[0]), recomb1[1])
recomb2 = (sorted(recomb2[0]), recomb2[1])
coal1 = (sorted(coal1[0]), coal1[1])
coal2 = (sorted(coal2[0]), coal2[1])
print
print (pos1, recomb1, coal1)
print (pos2, recomb2, coal2)
# check pos, leaves, time
assert pos1 == pos2
assert recomb1 == recomb2
assert coal1 == coal2
def test_arg_equal(arg, arg2):
# test recomb points
recombs = sorted(x.pos for x in arg if x.event == "recomb")
recombs2 = sorted(x.pos for x in arg2 if x.event == "recomb")
assert recombs == recombs2
# check local tree topologies
for (start, end), tree in arglib.iter_tree_tracks(arg):
pos = (start + end) / 2.0
arglib.remove_single_lineages(tree)
tree1 = tree.get_tree()
tree2 = arg2.get_marginal_tree(pos)
arglib.remove_single_lineages(tree2)
tree2 = tree2.get_tree()
hash1 = phylo.hash_tree(tree1)
hash2 = phylo.hash_tree(tree2)
print
print pos
print hash1
print hash2
assert hash1 == hash2
# check sprs
sprs1 = arglib.iter_arg_sprs(arg, use_leaves=True)
sprs2 = arglib.iter_arg_sprs(arg2, use_leaves=True)
for (pos1, recomb1, coal1), (pos2, recomb2, coal2) in izip(sprs1, sprs2):
recomb1 = (sorted(recomb1[0]), recomb1[1])
recomb2 = (sorted(recomb2[0]), recomb2[1])
coal1 = (sorted(coal1[0]), coal1[1])
coal2 = (sorted(coal2[0]), coal2[1])
print
print(pos1, recomb1, coal1)
print(pos2, recomb2, coal2)
# check pos, leaves, time
assert pos1 == pos2
assert recomb1 == recomb2
assert coal1 == coal2
def test_smcify_arg(self):
rho = 1.5e-8 # recomb/site/gen
l = 100000 # length of locus
k = 6 # number of lineages
n = 2*10000 # effective popsize
arg = arglib.sample_arg(k, n, rho, 0, l)
arg = arglib.smcify_arg(arg)
for pos, (rnode, rtime), (cnode, ctime) in arglib.iter_arg_sprs(arg):
self.assertNotEqual(rnode, cnode)
def test_iter_sprs(self):
rho = 1.5e-8 # recomb/site/gen
l = 100000 # length of locus
k = 6 # number of lineages
n = 2*10000 # effective popsize
arg = arglib.sample_arg(k, n, rho, 0, l)
for a, b in izip(arglib.iter_arg_sprs(arg),
arglib.iter_arg_sprs_simple(arg)):
self.assertEqual(a, b)
def test_trans_switch():
"""
Calculate transition probabilities for switch matrix
Only calculate a single matrix
"""
create_data = False
if create_data:
make_clean_dir('test/data/test_trans_switch')
# model parameters
k = 12
n = 1e4
rho = 1.5e-8 * 20
length = 1000
times = argweaver.get_time_points(ntimes=20, maxtime=200000)
popsizes = [n] * len(times)
ntests = 100
# generate test data
if create_data:
for i in range(ntests):
# Sample ARG with at least one recombination.
while True:
arg = argweaver.sample_arg_dsmc(k,
2 * n,
rho,
start=0,
end=length,
times=times)
if any(x.event == "recomb" for x in arg):
break
arg.write('test/data/test_trans_switch/%d.arg' % i)
for i in range(ntests):
print('arg', i)
arg = arglib.read_arg('test/data/test_trans_switch/%d.arg' % i)
argweaver.discretize_arg(arg, times)
recombs = [x.pos for x in arg if x.event == "recomb"]
pos = recombs[0]
tree = arg.get_marginal_tree(pos - .5)
rpos, r, c = next(arglib.iter_arg_sprs(arg, start=pos - .5))
spr = (r, c)
if not argweaverc.assert_transition_switch_probs(
tree, spr, times, popsizes, rho):
tree2 = tree.get_tree()
treelib.remove_single_children(tree2)
treelib.draw_tree_names(tree2, maxlen=5, minlen=5)
assert False
def arg_equal(arg, arg2):
# test recomb points
recombs = sorted(x.pos for x in arg if x.event == "recomb")
recombs2 = sorted(x.pos for x in arg2 if x.event == "recomb")
nose.tools.assert_equal(recombs, recombs2)
# check local tree topologies
for (start, end), tree in arglib.iter_local_trees(arg):
pos = (start + end) / 2.0
arglib.remove_single_lineages(tree)
tree1 = tree.get_tree()
tree2 = arg2.get_marginal_tree(pos)
arglib.remove_single_lineages(tree2)
tree2 = tree2.get_tree()
hash1 = phylo.hash_tree(tree1)
hash2 = phylo.hash_tree(tree2)
nose.tools.assert_equal(hash1, hash2)
# check sprs
sprs1 = arglib.iter_arg_sprs(arg, use_leaves=True)
sprs2 = arglib.iter_arg_sprs(arg2, use_leaves=True)
for (pos1, recomb1, coal1), (pos2, recomb2, coal2) in zip(sprs1, sprs2):
recomb1 = (sorted(recomb1[0]), recomb1[1])
recomb2 = (sorted(recomb2[0]), recomb2[1])
coal1 = (sorted(coal1[0]), coal1[1])
coal2 = (sorted(coal2[0]), coal2[1])
# check pos, leaves, time
nose.tools.assert_equal(pos1, pos2)
nose.tools.assert_equal(recomb1, recomb2)
nose.tools.assert_equal(coal1, coal2)
def arg_equal(arg, arg2):
# test recomb points
recombs = sorted(x.pos for x in arg if x.event == "recomb")
recombs2 = sorted(x.pos for x in arg2 if x.event == "recomb")
nose.tools.assert_equal(recombs, recombs2)
# check local tree topologies
for (start, end), tree in arglib.iter_local_trees(arg):
pos = (start + end) / 2.0
arglib.remove_single_lineages(tree)
tree1 = tree.get_tree()
tree2 = arg2.get_marginal_tree(pos)
arglib.remove_single_lineages(tree2)
tree2 = tree2.get_tree()
hash1 = phylo.hash_tree(tree1)
hash2 = phylo.hash_tree(tree2)
nose.tools.assert_equal(hash1, hash2)
# check sprs
sprs1 = arglib.iter_arg_sprs(arg, use_leaves=True)
sprs2 = arglib.iter_arg_sprs(arg2, use_leaves=True)
for (pos1, recomb1, coal1), (pos2, recomb2, coal2) in izip(sprs1, sprs2):
recomb1 = (sorted(recomb1[0]), recomb1[1])
recomb2 = (sorted(recomb2[0]), recomb2[1])
coal1 = (sorted(coal1[0]), coal1[1])
coal2 = (sorted(coal2[0]), coal2[1])
# check pos, leaves, time
nose.tools.assert_equal(pos1, pos2)
nose.tools.assert_equal(recomb1, recomb2)
nose.tools.assert_equal(coal1, coal2)
def test_iter_sprs_remove_thread(self):
rho = 1.5e-8 # recomb/site/gen
l = 100000 # length of locus
k = 6 # number of lineages
n = 2*10000 # effective popsize
arg = arglib.sample_arg(k, n, rho, 0, l)
remove_chroms = set("n%d" % (k-1))
keep = [x for x in arg.leaf_names() if x not in remove_chroms]
arg = arg.copy()
arglib.subarg_by_leaf_names(arg, keep)
for a, b in izip(arglib.iter_arg_sprs(arg),
arglib.iter_arg_sprs_simple(arg)):
self.assertEqual(a, b)
def test_iter_sprs_leaves(self):
rho = 1.5e-8 # recomb/site/gen
l = 100000 # length of locus
k = 40 # number of lineages
n = 2*10000 # effective popsize
arg = arglib.sample_arg(k, n, rho, 0, l)
for a, b in izip(arglib.iter_arg_sprs(arg, use_leaves=True),
arglib.iter_arg_sprs_simple(arg, use_leaves=True)):
a[1][0].sort()
a[2][0].sort()
b[1][0].sort()
b[2][0].sort()
self.assertEqual(a, b)
def test_trans_switch():
"""
Calculate transition probabilities for switch matrix
Only calculate a single matrix
"""
create_data = False
if create_data:
make_clean_dir('test/data/test_trans_switch')
# model parameters
k = 12
n = 1e4
rho = 1.5e-8 * 20
length = 1000
times = argweaver.get_time_points(ntimes=20, maxtime=200000)
popsizes = [n] * len(times)
ntests = 100
# generate test data
if create_data:
for i in range(ntests):
# Sample ARG with at least one recombination.
while True:
arg = argweaver.sample_arg_dsmc(
k, 2*n, rho, start=0, end=length, times=times)
if any(x.event == "recomb" for x in arg):
break
arg.write('test/data/test_trans_switch/%d.arg' % i)
for i in range(ntests):
print 'arg', i
arg = arglib.read_arg('test/data/test_trans_switch/%d.arg' % i)
argweaver.discretize_arg(arg, times)
recombs = [x.pos for x in arg if x.event == "recomb"]
pos = recombs[0]
tree = arg.get_marginal_tree(pos-.5)
rpos, r, c = arglib.iter_arg_sprs(arg, start=pos-.5).next()
spr = (r, c)
if not argweaverc.assert_transition_switch_probs(
tree, spr, times, popsizes, rho):
tree2 = tree.get_tree()
treelib.remove_single_children(tree2)
treelib.draw_tree_names(tree2, maxlen=5, minlen=5)
assert False
def layout_chroms(arg, start=None, end=None):
if start is None:
start = arg.start
if end is None:
end = arg.end
tree = arg.get_marginal_tree(start)
arglib.remove_single_lineages(tree)
last_pos = start
blocks = []
leaf_layout = []
layout_func = layout_tree_leaves
#layout_func = layout_tree_leaves_even
for spr in arglib.iter_arg_sprs(arg, start=start, end=end,
use_leaves=True):
print "layout", spr[0]
blocks.append([last_pos, spr[0]])
leaf_layout.append(layout_func(tree))
inorder = dict((n, i) for i, n in enumerate(inorder_tree(tree)))
# determine SPR nodes
rnode = arglib.arg_lca(tree, spr[1][0], spr[0])
cnode = arglib.arg_lca(tree, spr[2][0], spr[0])
# determine best side for adding new sister
left = (inorder[rnode] < inorder[cnode])
# apply spr
arglib.apply_spr(tree, rnode, spr[1][1], cnode, spr[2][1], spr[0])
# adjust sister
rindex = rnode.parents[0].children.index(rnode)
if left and rindex != 0:
rnode.parents[0].children.reverse()
last_pos = spr[0]
blocks.append([last_pos, end])
leaf_layout.append(layout_func(tree))
return blocks, leaf_layout
def layout_chroms(arg, start=None, end=None):
if start is None:
start = arg.start
if end is None:
end = arg.end
tree = arg.get_marginal_tree(start)
arglib.remove_single_lineages(tree)
last_pos = start
blocks = []
leaf_layout = []
layout_func = layout_tree_leaves
#layout_func = layout_tree_leaves_even
for spr in arglib.iter_arg_sprs(arg, start=start, end=end, use_leaves=True):
print "layout", spr[0]
blocks.append([last_pos, spr[0]])
leaf_layout.append(layout_func(tree))
inorder = dict((n, i) for i, n in enumerate(inorder_tree(tree)))
# determine SPR nodes
rnode = arglib.arg_lca(tree, spr[1][0], spr[0])
cnode = arglib.arg_lca(tree, spr[2][0], spr[0])
# determine best side for adding new sister
left = (inorder[rnode] < inorder[cnode])
# apply spr
arglib.apply_spr(tree, rnode, spr[1][1], cnode, spr[2][1], spr[0])
# adjust sister
rindex = rnode.parents[0].children.index(rnode)
if left and rindex != 0:
rnode.parents[0].children.reverse()
last_pos = spr[0]
blocks.append([last_pos, end])
leaf_layout.append(layout_func(tree))
return blocks, leaf_layout
def add_arg(self, arg):
nleaves = len(list(arg.leaves()))
times = self.times
assert times
eps = 1e-3
def get_local_children(node, pos, local):
return set(child for child in arg.get_local_children(node, pos) if child in local)
def get_parent(node, pos, local):
parent = arg.get_local_parent(node, pos)
while len(get_local_children(parent, pos, local)) == 1:
parent = arg.get_local_parent(parent, pos)
return parent
# add initial tree
tree = arg.get_marginal_tree(arg.start)
starts, ends, time_steps = count_tree_lineages(tree, times)
self.init_trees.append({"starts": starts, "ends": ends, "time_steps": time_steps})
# loop through sprs
for recomb_pos, (rnode, rtime), (cnode, ctime), local in arglib.iter_arg_sprs(arg, use_local=True):
i, _ = util.binsearch(times, ctime)
self.ncoals[i] += 1
recomb_node = arg[rnode]
broken_node = get_parent(recomb_node, recomb_pos - eps, local)
coals = [0.0] + [node.age for node in local if len(get_local_children(node, recomb_pos - eps, local)) == 2]
coals.sort()
nlineages = range(nleaves, 0, -1)
assert len(nlineages) == len(coals)
# subtract broken branch
r = coals.index(recomb_node.age)
r2 = coals.index(broken_node.age)
for i in range(r, r2):
nlineages[i] -= 1
# get average number of branches in the time interval
data = zip(coals, nlineages)
for t in times[1:]:
data.append((t, "time step"))
data.sort()
lineages_per_time = []
counts = []
last_lineages = 0
last_time = 0.0
for a, b in data:
if b != "time step":
if a > last_time:
counts.append((last_lineages, a - last_time))
last_lineages = b
else:
counts.append((last_lineages, a - last_time))
s = sum(u * v for u, v in counts)
total_time = sum(v for u, v in counts)
if s == 0.0:
lineages_per_time.append(last_lineages)
else:
lineages_per_time.append(s / total_time)
counts = []
last_time = a
assert len(lineages_per_time) == len(self.time_steps)
r, _ = util.binsearch(times, rtime)
c, _ = util.binsearch(times, ctime)
for j in range(r, c):
self.k_lineages[j] += lineages_per_time[j]
def add_arg(self, arg):
nleaves = len(list(arg.leaves()))
times = self.times
assert times
eps = 1e-3
def get_local_children(node, pos, local):
return set(child for child in arg.get_local_children(node, pos)
if child in local)
def get_parent(node, pos, local):
parent = arg.get_local_parent(node, pos)
while len(get_local_children(parent, pos, local)) == 1:
parent = arg.get_local_parent(parent, pos)
return parent
# add initial tree
tree = arg.get_marginal_tree(arg.start)
starts, ends, time_steps = count_tree_lineages(tree, times)
self.init_trees.append({
"starts": starts,
"ends": ends,
"time_steps": time_steps
})
# loop through sprs
for recomb_pos, (rnode, rtime), (cnode, ctime), local in \
arglib.iter_arg_sprs(arg, use_local=True):
i, _ = util.binsearch(times, ctime)
self.ncoals[i] += 1
recomb_node = arg[rnode]
broken_node = get_parent(recomb_node, recomb_pos - eps, local)
coals = [0.0] + [
node.age for node in local
if len(get_local_children(node, recomb_pos - eps, local)) == 2
]
coals.sort()
nlineages = list(range(nleaves, 0, -1))
assert len(nlineages) == len(coals)
# subtract broken branch
r = coals.index(recomb_node.age)
r2 = coals.index(broken_node.age)
for i in range(r, r2):
nlineages[i] -= 1
# get average number of branches in the time interval
data = list(zip(coals, nlineages))
for t in times[1:]:
data.append((t, "time step"))
data.sort()
lineages_per_time = []
counts = []
last_lineages = 0
last_time = 0.0
for a, b in data:
if b != "time step":
if a > last_time:
counts.append((last_lineages, a - last_time))
last_lineages = b
else:
counts.append((last_lineages, a - last_time))
s = sum(u * v for u, v in counts)
total_time = sum(v for u, v in counts)
if s == 0.0:
lineages_per_time.append(last_lineages)
else:
lineages_per_time.append(s / total_time)
counts = []
last_time = a
assert len(lineages_per_time) == len(self.time_steps)
r, _ = util.binsearch(times, rtime)
c, _ = util.binsearch(times, ctime)
for j in range(r, c):
self.k_lineages[j] += lineages_per_time[j]