diff --git a/tasks/betweenness_centrality.py b/tasks/betweenness_centrality.py index 06d4ca0b6ba384e4db02aff9ca5f4a192b3e7879..deba02742d9647ce1525a5944ad396b9608f5f7d 100755 --- a/tasks/betweenness_centrality.py +++ b/tasks/betweenness_centrality.py @@ -181,6 +181,7 @@ def betweenness_centrality(task_hook: TaskHook): g, seed_ids, drug_ids = read_graph_tool_graph( filename, seeds, + id_space, max_deg, include_indirect_drugs, include_non_approved_drugs, diff --git a/tasks/keypathwayminer_task.py b/tasks/keypathwayminer_task.py index 639d589903a8c386d11baed7b1499fea232a1261..3e5099a185939c703876955d0044d4b5f1a4bd7e 100755 --- a/tasks/keypathwayminer_task.py +++ b/tasks/keypathwayminer_task.py @@ -213,7 +213,7 @@ def kpm_task(task_hook: TaskHook): if id_space == 'ensembl': node_map[node.uniprot_code] = [ensg.name for ensg in EnsemblGene.objects.filter(protein_id=node.id)] - flat_map = lambda f, xs: [y for ys in xs for y in f(ys)] + flat_map = lambda f, xs: (y for ys in xs for y in f(ys)) network["nodes"] = flat_map(lambda uniprot: node_map[uniprot], network["nodes"]) network["edges"] = list(map( diff --git a/tasks/util/read_graph_tool_graph.py b/tasks/util/read_graph_tool_graph.py index 9901ae1a477e841831dc1fd7d445da28254c51b0..35a89c4a9426956e05f4ae93d7fb8d019ec9b426 100755 --- a/tasks/util/read_graph_tool_graph.py +++ b/tasks/util/read_graph_tool_graph.py @@ -92,8 +92,9 @@ def read_graph_tool_graph(file_path, seeds, id_space, max_deg, include_indirect_ deleted_edges = [] - if ( - drug_ids and not include_indirect_drugs): # If only_direct_drugs should be included, remove any drug-protein edges that the drug is not a direct neighbor of any seeds + # If only_direct_drugs should be included, remove any drug-protein edges that the drug is not a direct neighbor of + # any seeds + if drug_ids and not include_indirect_drugs: direct_drugs = set() for edge in g.edges(): if g.vertex_properties["type"][edge.target()] == d_type and edge.source() in seed_ids: