def evolve_to_current_time(node, finalize=False):
if node is None:
return
viruses = [virus for virus in node.viruses()]
for virus in viruses:
time = GC.time - virus.get_time()
if time > 0:
node.remove_virus(virus)
try:
command = [
GC.dualbirth_path,
str(GC.rate_A),
str(GC.rate_B), '-t',
str(time)
]
if GC.random_number_seed is not None:
command += ['-s', str(GC.random_number_seed)]
GC.random_number_seed += 1
treestr = check_output(command).decode()
except FileNotFoundError:
from os import chdir
chdir(GC.START_DIR)
assert False, "dualbirth executable was not found: %s" % GC.dualbirth_path
tree = read_tree_newick(treestr)
virus.set_time(virus.get_time() + tree.root.edge_length)
for c in tree.root.children:
GC.treenode_add_child(virus, c, node)
def evolve_to_current_time(node, finalize=False):
viruses = [virus for virus in node.viruses()]
for virus in viruses:
time = GC.time - virus.get_time()
if time > 0:
node.remove_virus(virus)
success = False
for _ in range(100):
tree = birth_death_tree(GC.bd_birth,
GC.bd_death,
birth_rate_sd=GC.bd_birth_sd,
death_rate_sd=GC.bd_death_sd,
max_time=time,
repeat_until_success=True,
rng=rng)
if tree.seed_node.num_child_nodes() > 1:
success = True
break
assert success, "Failed to create non-empty Birth-Death tree after 100 attempts. Perhaps try a higher birth rate or lower death rate?"
virus.set_time(virus.get_time() + tree.seed_node.edge_length)
for c in tree.seed_node.child_node_iter():
GC.treenode_add_child(virus, c, node)