Divide the memory use by 7; computation time reduced by 10 sec

command_line/cadbiom_cmd/interaction_graph.py

@@ -230,9 +230,9 @@ def build_interactions(filtered_macs, binary_interactions):
         filtered_binary_interactions: Interactions between molecules of interest and frontier places that are not genes in trajectories
     """
 
-    genes_stimuli_interactions = list()
-    genes_interactions = list()
-    stimulis_interactions = list()
+    genes_stimuli_interactions = Counter()
+    genes_interactions = Counter()
+    stimulis_interactions = Counter()
     # All genes in frontier places
     all_genes = set()
     # All other entities in frontier places
@@ -254,11 +254,11 @@ def build_interactions(filtered_macs, binary_interactions):
         # For every solution composed of frontier places,
         # compute binary interactions between:
         # genes and stimulis
-        genes_stimuli_interactions += list(it.product(genes, stimuli))
+        genes_stimuli_interactions.update(it.product(genes, stimuli))
         # genes two by two
-        genes_interactions += list(it.combinations(genes, 2))
+        genes_interactions.update(it.combinations(genes, 2))
         # stimulis two by two
-        stimulis_interactions += list(it.combinations(stimuli, 2))
+        stimulis_interactions.update(it.combinations(stimuli, 2))
 
 #    print("genes/stimulis interactions:", genes_stimuli_interactions)
 #    print("genes interactions:", genes_interactions)
@@ -312,20 +312,13 @@ def build_interactions(filtered_macs, binary_interactions):
         filtered_binary_interactions
 
 
-def build_graph(all_genes, all_stimuli, genes_interactions,
-                stimulis_interactions,
-                genes_stimuli_interactions,
-                filtered_binary_interactions):
+def build_graph(all_genes, all_stimuli, unique_genes_interactions,
+                unique_stimulis_interactions,
+                unique_genes_stimuli_interactions,
+                unique_filtered_binary_interactions):
     """
     """
 
-    unique_genes_interactions = Counter(genes_interactions)
-    unique_stimulis_interactions = Counter(stimulis_interactions)
-    unique_genes_stimuli_interactions = Counter(genes_stimuli_interactions)
-    unique_filtered_binary_interactions = filtered_binary_interactions
-    #print(unique_genes_interactions, unique_stimulis_interactions,
-    #      unique_genes_stimuli_interactions, unique_filtered_binary_interactions)
-
     # Counter update...
     nodes_count = Counter(it.chain(*unique_genes_interactions.keys()))
     nodes_count.update(it.chain(*unique_stimulis_interactions.keys()))