from tasks.task_hook import TaskHook
from tasks.util.custom_edges import add_edges
from tasks.util.steiner_tree import steiner_tree
from tasks.util.find_bridges import find_bridges
from tasks.util.read_graph_tool_graph import read_graph_tool_graph
from tasks.util.edge_weights import edge_weights
import os.path
import graph_tool as gt
import graph_tool.util as gtu
import sys
def multi_steiner(task_hook: TaskHook):
# Type: List of str
# Semantics: Names of the seed proteins. Use UNIPROT AC for host proteins, and
# names of the format SARS_CoV2_<IDENTIFIER> (tree_edge.g., SARS_CoV2_ORF6) for
# virus proteins.
# Reasonable default: None, has to be selected by user via "select for analysis"
# utility in frontend.
# Acceptable values: UNIPROT ACs, identifiers of viral proteins.
seeds = task_hook.parameters["seeds"]
# Since we get the LCC of the graphs from read_graph_tool_graph, no need for the following two lines
# nodes_not_in_lcc = {'D3W0D1', 'O15178', 'O60542', 'O60609', 'O60882', 'Q5T4W7', 'Q6UVW9', 'Q6UW32', 'Q6UWQ7', 'Q6UXB1', 'Q7RTX0', 'Q7RTX1', 'Q8TE23', 'Q9GZZ7', 'Q9H2W2', 'Q9H665', 'Q9NZW4'}
# seeds = [node for node in set(seeds).difference(nodes_not_in_lcc)]
seeds.sort()
# Type: str.
# Semantics: The virus strain for which the analysis should be run.
# Example: "SARS_CoV2"
# Reasonable default: None, has to be specified by the caller.
### Acceptable values: "SARS_CoV2", ...
# strain_or_drugs = task_hook.parameters.get("strain_or_drugs", "SARS_CoV2")
# Acceptable values: "PPI", "PPDr"
# target_or_drugs = task_hook.parameters.get("target_or_drugs", "PPI")
# Type: list of str.
# Semantics: The datasets which should be considered for the analysis.
# Example: ["Krogan", "TUM"].
# Note: If empty, all available datasets are used.
# Reasonable default: [].
# Acceptable values: "Krogan", "TUM".
# datasets = task_hook.parameters.get("datasets", [])
# Type: list of str.
# Semantics: Virus-host g_edge types which should be ignored for the analysis.
# Example: ["Overexpression"].
# Note: If empty, all available g_edge types are used.
# Reasonable default: [].
# Acceptable values: "AP-MS", "overexpression".
# ignored_edge_types = task_hook.parameters.get("ignored_edge_types", [])
# Type bool.
# Semantics: Ignore viral proteins which are not selected as seeds.
# Example: False.
# Reasonable default: False.
# Has no effect when the algorithm is used for ranking drugs.
# ignore_non_seed_baits = task_hook.parameters.get("ignore_non_seed_baits", False)
# Type: int.
# Semantics: Number of steiner trees to return.
# Example: 10.
# Reasonable default: 5.
# Acceptable values: integers n with 0 < n < 25.
num_trees = task_hook.parameters.get("num_trees", 5)
# Type: float.
# Semantics: The error tolerance of the subsequent Steiner trees w.r.t. the first one in percent.
# Example: 10
# Reasonable default: 10.
# Acceptable values: floats x >= 0.
tolerance = task_hook.parameters.get("tolerance", 10)
# Type: int.
# Semantics: All nodes with degree > max_deg * g.num_vertices() are ignored.
# Example: 39.
# Reasonable default: sys.maxsize.
# Acceptable values: Positive integers.
max_deg = task_hook.parameters.get("max_deg", sys.maxsize)
# Type: float.
# Semantics: Penalty parameter for hubs. Set edge weight to 1 + (hub_penalty / 2) (e.source.degree + e.target.degree)
# Example: 0.5.
# Reasonable default: 0.
# Acceptable values: Floats between 0 and 1.
hub_penalty = task_hook.parameters.get("hub_penalty", 0.0)
# Type: int.
# Semantics: Number of threads used for running the analysis.
# Example: 1.
# Reasonable default: 1.
# Note: We probably do not want to expose this parameter to the user.
num_threads = task_hook.parameters.get("num_threads", 1)
ppi_dataset = task_hook.parameters.get("ppi_dataset")
pdi_dataset = task_hook.parameters.get("pdi_dataset")
search_target = task_hook.parameters.get("target", "drug-target")
node_name_attribute = "internal_id" # nodes in the input network which is created from RepoTrialDB have primaryDomainId as name attribute
custom_edges = task_hook.parameters.get("custom_edges", False)
# Set number of threads if OpenMP support is enabled.
if gt.openmp_enabled():
gt.openmp_set_num_threads(num_threads)
# Parsing input file.
task_hook.set_progress(0 / (float(num_trees + 3)), "Parsing input.")
id_space = task_hook.parameters["config"].get("identifier", "symbol")
filename = f"{id_space}_{ppi_dataset['name']}-{pdi_dataset['name']}"
if ppi_dataset['licenced'] or pdi_dataset['licenced']:
filename += "_licenced"
filename = os.path.join(task_hook.data_directory, filename + ".gt")
print(filename)
g, seed_ids, _ = read_graph_tool_graph(filename, seeds, id_space, max_deg, target=search_target)
if custom_edges:
edges = task_hook.parameters.get("input_network")['edges']
g = add_edges(g, edges)
seed_map = {g.vertex_properties[node_name_attribute][node]: node for node in seed_ids}
task_hook.set_progress(1 / (float(num_trees + 3)), "Computing edge weights.")
weights = edge_weights(g, hub_penalty)
# Find first steiner trees
seeds = list(filter(lambda s: s in seed_map, seeds))
task_hook.set_progress(2 / (float(num_trees + 3)), "Computing Steiner tree 1 of {}.".format(num_trees))
first_tree = steiner_tree(g, seeds, seed_map, weights, hub_penalty > 0)
num_found_trees = 1
tree_edges = []
for tree_edge in first_tree.edges():
source_name = first_tree.vertex_properties[node_name_attribute][first_tree.vertex_index[tree_edge.source()]]
target_name = first_tree.vertex_properties[node_name_attribute][first_tree.vertex_index[tree_edge.target()]]
tree_edges.append((gtu.find_vertex(g, prop=g.vertex_properties[node_name_attribute], match=source_name)[0], gtu.find_vertex(g, prop=g.vertex_properties[node_name_attribute], match=target_name)[0]))
cost_first_tree = sum([weights[g.edge(source, target)] for source, target in tree_edges])
returned_nodes = set(int(gtu.find_vertex(g, prop=g.vertex_properties[node_name_attribute], match=first_tree.vertex_properties[node_name_attribute][node])[0]) for node in range(first_tree.num_vertices()))
if num_trees > 1:
is_bridge = find_bridges(g)
edge_filter = g.new_edge_property("boolean", True)
found_new_tree = True
while len(tree_edges) > 0:
if found_new_tree:
task_hook.set_progress(float(num_found_trees + 2) / (float(num_trees + 3)), "Computing Steiner tree {} of {}.".format(num_found_trees + 1, num_trees))
found_new_tree = False
tree_edge = tree_edges.pop()
g_edge = g.edge(tree_edge[0], tree_edge[1])
if not is_bridge[g_edge]:
edge_filter[g_edge] = False
g.set_edge_filter(edge_filter)
next_tree = steiner_tree(g, seeds, seed_map, weights, hub_penalty > 0)
next_tree_edges = set()
for next_tree_edge in next_tree.edges():
source_name = next_tree.vertex_properties[node_name_attribute][next_tree.vertex_index[next_tree_edge.source()]]
target_name = next_tree.vertex_properties[node_name_attribute][next_tree.vertex_index[next_tree_edge.target()]]
next_tree_edges.add((gtu.find_vertex(g, prop=g.vertex_properties[node_name_attribute], match=source_name)[0],gtu.find_vertex(g, prop=g.vertex_properties[node_name_attribute], match=target_name)[0]))
cost_next_tree = sum([weights[g.edge(source, target)] for source, target in next_tree_edges])
if cost_next_tree <= cost_first_tree * ((100.0 + tolerance) / 100.0):
found_new_tree = True
num_found_trees += 1
for node in range(next_tree.num_vertices()):
returned_nodes.add(int(gtu.find_vertex(g, prop=g.vertex_properties[node_name_attribute],match=next_tree.vertex_properties[node_name_attribute][node])[0]))
removed_edges = []
for source, target in tree_edges:
if not ((source, target) in set(next_tree_edges)) or ((target, source) in set(next_tree_edges)):
removed_edges.append((source, target))
for edge in removed_edges:
tree_edges.remove(edge)
g.clear_filters()
edge_filter[g_edge] = True
if num_found_trees >= num_trees:
break
task_hook.set_progress((float(num_trees + 2)) / (float(num_trees + 3)), "Formatting results")
returned_edges = []
for node in returned_nodes:
for neighbor in g.get_all_neighbors(node):
if int(neighbor) > node and int(neighbor) in returned_nodes:
returned_edges.append((node, int(neighbor)))
accepted_nodes = [g.vertex_properties[node_name_attribute][node] for node in returned_nodes]
subgraph = {"nodes": accepted_nodes,
"edges": [{"from": g.vertex_properties[node_name_attribute][source], "to": g.vertex_properties[node_name_attribute][target]} for
source, target in returned_edges]}
node_types = {g.vertex_properties[node_name_attribute][node]: g.vertex_properties["type"][node] for node in returned_nodes}
is_seed = {g.vertex_properties[node_name_attribute][node]: node in set(seed_ids) for node in returned_nodes}
task_hook.set_results({
"network": subgraph,
"node_attributes": {"node_types": node_types, "is_seed": is_seed},
"taget_nodes":accepted_nodes,
'gene_interaction_dataset': ppi_dataset,
'drug_interaction_dataset': pdi_dataset
})