def get_all_paths_to_root(node_id: str,
ontology: Ontology,
min_distance_from_root: int = 0,
relations: List[str] = None,
nodeids_blacklist: List[str] = None,
previous_path: Union[None, List[str]] = None,
root_node=None) -> Set[Tuple[str]]:
"""get all possible paths connecting a go term to its root terms
Args:
node_id (str): a valid GO id for the starting term
ontology (Ontology): the go ontology
min_distance_from_root (int): return only terms at a specified minimum distance from root terms
relations (List[str]): the list of relations to be used
nodeids_blacklist (List[str]): a list of node ids to exclude from the paths
previous_path (Union[None, List[str]]): the path to get to the current node
Returns:
Set[Tuple[str]]: the set of paths connecting the specified term to its root terms, each of which contains a
sequence of terms ids
"""
if previous_path is None:
previous_path = []
new_path = previous_path[:]
if not nodeids_blacklist or node_id not in nodeids_blacklist:
new_path.append(node_id)
parents = [
parent
for parent in ontology.parents(node=node_id, relations=relations)
if ontology.node(parent)["depth"] >= min_distance_from_root
]
parents_same_root = []
if root_node:
for parent in parents:
parent_root = None
if "meta" in parent and "basicPropertyValues" in parent["meta"]:
for basic_prop_val in parent["meta"]["basicPropertyValues"]:
if basic_prop_val["pred"] == "OIO:hasOBONamespace":
parent_root = basic_prop_val["val"]
if parent_root and parent_root == root_node:
parents_same_root.append(parent)
parents = parents_same_root
if len(parents) > 0:
# go up the tree, following a depth first visit
paths_to_return = set()
for parent in parents:
for path in get_all_paths_to_root(
node_id=parent,
ontology=ontology,
previous_path=new_path,
min_distance_from_root=min_distance_from_root,
relations=relations,
nodeids_blacklist=nodeids_blacklist,
root_node=root_node):
paths_to_return.add(path)
return paths_to_return
if len(new_path) == 0:
return {(node_id, )}
else:
return {tuple(new_path)}
def _set_num_subsumers_in_subgraph(ontology: Ontology,
root_id: str,
relations: List[str] = None):
if "num_subsumers" not in ontology.node(root_id):
parents = set(ontology.parents(root_id))
parents.discard(root_id)
parents = list(parents)
if not parents or all(
["set_subsumers" in ontology.node(parent) for parent in parents]):
subsumers = {subsumer for parent in parents for subsumer in ontology.node(parent)["set_subsumers"]} | \
{root_id}
ontology.node(root_id)["num_subsumers"] = len(subsumers)
ontology.node(root_id)["set_subsumers"] = subsumers
for child_id in ontology.children(node=root_id):
_set_num_subsumers_in_subgraph(ontology, child_id, relations)
def _set_num_subsumers_in_subgraph(ontology: Ontology,
root_id: str,
relations: List[str] = None):
parents = ontology.parents(root_id)
if len(parents) == 1:
ontology.node(root_id)["num_subsumers"] = ontology.node(
parents[0])["num_subsumers"] + 1
else:
ontology.node(root_id)["num_subsumers"] = len(
ontology.ancestors(node=root_id,
relations=relations,
reflexive=True))
for child_id in ontology.children(node=root_id, relations=relations):
_set_num_subsumers_in_subgraph(ontology=ontology,
root_id=child_id,
relations=relations)
def neighbor_by_relation(ontology_graph: ontol.Ontology, term, relation):
return ontology_graph.parents(term, relations=[relation])