diff --git a/tasks/first_neighbor.py b/tasks/first_neighbor.py index 6b485cb..44e9774 100644 --- a/tasks/first_neighbor.py +++ b/tasks/first_neighbor.py @@ -63,6 +63,7 @@ def first_neighbor(task_hook: TaskHook): custom_edges = task_hook.parameters.get("custom_edges", False) no_default_edges = task_hook.parameters.get("exclude_drugstone_ppi_edges", False) + allow_self_references = task_hook.parameters["config"].get("selfReferences", False) # Set number of threads if OpenMP support is enabled. @@ -214,6 +215,9 @@ def first_neighbor(task_hook: TaskHook): } edges.append(edge) + if not allow_self_references: + edges = [edge for edge in edges if edge["from"] != edge["to"]] + # Filter nodes to keep only upstream regulators if parameter is set only_upstream_regulators = task_hook.parameters.get("only_upstream_regulators", False) is_omnipath = ppi_dataset["name"] == "OmniPath" diff --git a/tasks/leiden_clustering.py b/tasks/leiden_clustering.py index f45e9ef..2bb5dc2 100644 --- a/tasks/leiden_clustering.py +++ b/tasks/leiden_clustering.py @@ -158,7 +158,7 @@ def leiden_clustering(task_hook: TaskHook): # If seed is not set, generate a random seed. if seed is None: seed = random.randint(1, 10000) - task_hook.parameters["seed"] = seed + task_hook.parameters["seed"] = seed # Parsing input file. task_hook.set_progress(1 / 4.0, "Parsing input.") diff --git a/tasks/louvain_clustering.py b/tasks/louvain_clustering.py index 13258d7..49d27db 100644 --- a/tasks/louvain_clustering.py +++ b/tasks/louvain_clustering.py @@ -157,7 +157,7 @@ def louvain_clustering(task_hook: TaskHook): # If seed is not set, generate a random seed. if seed is None: seed = random.randint(1, 10000) - task_hook.parameters["seed"] = seed + task_hook.parameters["seed"] = seed # Parsing input file. task_hook.set_progress(1 / 4.0, "Parsing input.")