def leave_node(key, node, population, cofmat):
if node_is_non_admixture(node):
return [follow_branch(parent_key=node[0],branch=(key,0), population=population, cofmat=cofmat)]
else:
new_pop=population.remove_partition(1.0-node[2])
return [follow_branch(parent_key=node[0],branch=(key,0), population=population, cofmat=cofmat, dependent='none'), #changed dependent='none' to go to most loose restriction that still makes sense. To go back,put dependent=node[1
follow_branch(parent_key=node[1],branch=(key,1), population=new_pop, cofmat=cofmat, dependent='none')]
def leave_node_and_check_admixtures(key, node, population, covmat):
if node_is_non_admixture(node):
return [
follow_branch(parent_key=node[0],
branch_length=node[3],
population=population,
covmat=covmat)
], []
else:
members = population.members[:]
new_pop = population.remove_partition(1.0 - node[2])
return [
follow_branch(
parent_key=node[0],
branch_length=node[3],
population=population,
covmat=covmat,
dependent='none'
), #changed dependent='none' to go to most loose restriction that still makes sense. To go back,put dependent=node[1
follow_branch(parent_key=node[1],
branch_length=node[4],
population=new_pop,
covmat=covmat,
dependent='none')
], members
def leave_node(key, node, population, target_nodes, follow_branch):
if node_is_non_admixture(node):
return [
follow_branch(parent_key=node[0],
branch=0,
population=population,
target_nodes=target_nodes,
child_key=key)
]
else:
new_pop = population.remove_partition(1.0 - node[2])
return [
follow_branch(
parent_key=node[0],
branch=0,
population=population,
target_nodes=target_nodes,
child_key=key,
dependent='none'
), #changed dependent='none' to go to most loose restriction that still makes sense. To go back,put dependent=node[1
follow_branch(parent_key=node[1],
branch=1,
population=new_pop,
target_nodes=target_nodes,
child_key=key,
dependent='none')
]
def _check_node(tree, key, direction):
parent_key = tree[key][direction]
return ((parent_key == 'r' or node_is_non_admixture(tree[parent_key]))
and not parent_is_spouse(tree, key, other_branch(direction))
and (parent_key == 'r'
or not halfbrother_is_uncle(tree, key, parent_key))
and (parent_key == 'r'
or not (parent_is_spouse(tree, key, direction)
and parent_is_sibling(tree, key, direction))))
def _add_to_waiting(dic, add, tree):
key, pop, dep = add
if key in dic: #this means that the node is a coalescence node
dic[key][0][1] = pop
dic[key][1][1] = dep
else:
if key == 'r' or node_is_non_admixture(tree[key]):
dic[key] = [[pop, None], [dep, "empty"]]
else:
dic[key] = [[pop], [dep]]
return dic
def get_possible_regrafters(tree):
res = []
for key in tree:
parents = get_real_parents(tree[key])
#print parents
for branch, parent in enumerate(parents):
#print key,(not is_root(parent)),node_is_non_admixture(tree[parent]),(not has_child_admixture(tree, parent))
#if (not is_root(parent)) and node_is_non_admixture(tree[parent]) and (not has_child_admixture(tree, parent)):
if parent == 'r' or (node_is_non_admixture(tree[parent]) and
not halfbrother_is_uncle(tree, key, parent)):
res.append((key, branch))
return res