From a86879a162b08abeec7166c04b7949ed96c4a05d Mon Sep 17 00:00:00 2001
From: AndiMajore <andi.majore@googlemail.com>
Date: Tue, 26 Jul 2022 17:25:34 +0200
Subject: [PATCH] betweenes centrality fixed
Former-commit-id: c3e7bd3cf65e180f9153272087c802aad19e0061 [formerly e34d9a36054a15f0fe8bd3461c66f75fd333e1ee]
Former-commit-id: bd35491f003f79dc5b47609a542b3e2a636f02b5
---
tasks/betweenness_centrality.py | 1 +
tasks/keypathwayminer_task.py | 2 +-
tasks/util/read_graph_tool_graph.py | 5 +++--
3 files changed, 5 insertions(+), 3 deletions(-)
diff --git a/tasks/betweenness_centrality.py b/tasks/betweenness_centrality.py
index 06d4ca0..deba027 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 639d589..3e5099a 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 9901ae1..35a89c4 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:
--
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