tried to simplify read_graph_tool_graph

Former-commit-id: b30ddcce5a74933259b2d844f3576058274aa881 [formerly 3ffcd24d7bd7ab56f2a38772eb665da6ff7af3c6]
Former-commit-id: 5a3c12455d37f3ad1b696e60d178c5f2a4e66e3e

tasks/util/read_graph_tool_graph.py

@@ -91,13 +91,20 @@ def read_graph_tool_graph(file_path, seeds, max_deg, include_indirect_drugs=Fals
             print(int(drug))
         for edge in g.edges():
             if g.edge_properties["type"][edge] == 'drug-protein':
-                if g.vertex_properties["type"][edge.target()] == d_type and edge.target() not in direct_drugs:
+                if g.vertex_properties["type"][edge.target()] == d_type:
+                    indir_drug = edge.target() not in direct_drugs
+                    not_seed = edge.source() not in seed_ids
+                    if indir_drug or not_seed:
                         deleted_edges.append(edge)
-                    if int(edge.target()) in drug_ids:
+                    if indir_drug and int(edge.target()) in drug_ids:
                         drug_ids.remove(int(edge.target()))
-                elif g.vertex_properties["type"][edge.source()] == d_type and edge.source() not in direct_drugs:
+
+                elif g.vertex_properties["type"][edge.source()] == d_type and edge.source() not in direct_drugs or edge.target() not in seed_ids:
+                    indir_drug = edge.source() not in direct_drugs
+                    not_seed = edge.target() not in seed_ids
+                    if indir_drug or not_seed:
                         deleted_edges.append(edge)
-                    if int(edge.source()) in drug_ids:
+                    if indir_drug and int(edge.source()) in drug_ids:
                         drug_ids.remove(int(edge.source()))
 
     g.set_fast_edge_removal(fast=True)