def traceback(self):
# Run the traceback.
m = self.ts.num_sites
match = np.zeros(m, dtype=int)
recombination_tree = np.zeros(self.ts.num_nodes, dtype=int) - 1
tree = tskit.Tree(self.ts)
tree.last()
current_node = -1
rr_index = len(self.recombination_required) - 1
for site in reversed(self.ts.sites()):
while tree.interval[0] > site.position:
tree.prev()
assert tree.interval[0] <= site.position < tree.interval[1]
# Fill in the recombination tree
j = rr_index
while self.recombination_required[j][0] == site.id:
u, required = self.recombination_required[j][1:]
recombination_tree[u] = required
j -= 1
if current_node == -1:
current_node = self.choose_sample(site.id, tree)
match[site.id] = current_node
# Now traverse up the tree from the current node. The first marked node
# we meet tells us whether we need to recombine.
u = current_node
while u != -1 and recombination_tree[u] == -1:
u = tree.parent(u)
assert u != -1
if recombination_tree[u] == 1:
# Need to switch at the next site.
current_node = -1
# Reset the nodes in the recombination tree.
j = rr_index
while self.recombination_required[j][0] == site.id:
u, required = self.recombination_required[j][1:]
recombination_tree[u] = -1
j -= 1
rr_index = j
return match
def __init__(self, ts, rho, mu, alleles, precision=10):
self.ts = ts
self.mu = mu
self.rho = rho
self.alleles = check_alleles(alleles, ts.num_sites)
self.precision = precision
# The array of ValueTransitions.
self.T = []
# indexes in to the T array for each node.
self.T_index = np.zeros(ts.num_nodes, dtype=int) - 1
# The number of nodes underneath each element in the T array.
self.N = np.zeros(ts.num_nodes, dtype=int)
# Efficiently compute the allelic state at a site
self.allelic_state = np.zeros(ts.num_nodes, dtype=int) - 1
# Diffs so we can can update T and T_index between trees.
self.edge_diffs = self.ts.edge_diffs()
self.parent = np.zeros(self.ts.num_nodes, dtype=int) - 1
self.tree = tskit.Tree(self.ts)
self.output = None
def moving_along_tree_sequence():
ts = msprime.simulate(5, recombination_rate=1, random_seed=42)
print(f"Tree sequence has {ts.num_trees} trees")
print()
for tree in ts.trees():
print("Tree {} covers [{:.2f}, {:.2f}); TMRCA = {:.4f}".format(
tree.index, *tree.interval, tree.time(tree.root)))
print()
for tree in reversed(ts.trees()):
print("Tree {} covers [{:.2f}, {:.2f}); TMRCA = {:.4f}".format(
tree.index, *tree.interval, tree.time(tree.root)))
print()
for tree in list(ts.trees()):
print("Tree {} covers [{:.2f}, {:.2f}): id={:x}".format(
tree.index, *tree.interval, id(tree)))
print()
for tree in ts.aslist():
print("Tree {} covers [{:.2f}, {:.2f}): id={:x}".format(
tree.index, *tree.interval, id(tree)))
print()
tree = ts.at(0.5)
print("Tree {} covers [{:.2f}, {:.2f}): id={:x}".format(
tree.index, *tree.interval, id(tree)))
tree = ts.at_index(0)
print("Tree {} covers [{:.2f}, {:.2f}): id={:x}".format(
tree.index, *tree.interval, id(tree)))
tree = ts.at_index(-1)
print("Tree {} covers [{:.2f}, {:.2f}): id={:x}".format(
tree.index, *tree.interval, id(tree)))
print()
tree = tskit.Tree(ts)
tree.seek_index(ts.num_trees // 2)
print("Tree {} covers [{:.2f}, {:.2f})".format(tree.index, *tree.interval))
tree.seek(0.95)
print("Tree {} covers [{:.2f}, {:.2f})".format(tree.index, *tree.interval))
print()
tree.prev()
print("Tree {} covers [{:.2f}, {:.2f})".format(tree.index, *tree.interval))
tree.next()
print("Tree {} covers [{:.2f}, {:.2f})".format(tree.index, *tree.interval))
print()
tree = tskit.Tree(ts)
print(f"Tree {tree.index}: parent_dict = {tree.parent_dict}")
tree.first()
print(f"Tree {tree.index}: parent_dict = {tree.parent_dict}")
tree.prev()
print(f"Tree {tree.index}: parent_dict = {tree.parent_dict}")
tree = tskit.Tree(ts)
while tree.next():
print("Tree {} covers [{:.2f}, {:.2f})".format(tree.index,
*tree.interval))
print("After loop: tree index =", tree.index)
while tree.prev():
print("Tree {} covers [{:.2f}, {:.2f})".format(tree.index,
*tree.interval))
