PEP8 review

command_line/cadbiom_cmd/cadbiom_cmd.py

@@ -254,7 +254,7 @@ def main():
              "While there will be 1 process per line (per logical formula "
              "on each line)")
     parser_input_file.add_argument('--output', action=ReadableDir, nargs='?',
-        default='result/', help="Output directory.")
+                                   default='result/', help="Output directory.")
 
     # default: False
     parser_input_file.add_argument('--combinations', action='store_true',
@@ -335,8 +335,7 @@ def main():
         'json_2_interaction_graph',
         help=json_2_interaction_graph.__doc__,
         formatter_class=argparse.ArgumentDefaultsHelpFormatter)
-    parser_json_2_interaction_graph.add_argument('molecules_of_interest',
-        nargs='+',
+    parser_json_2_interaction_graph.add_argument('molecules_of_interest', nargs='+',
         help="One or multiple molecule of interest to search in the trajectories"
              " of every solutions")
     parser_json_2_interaction_graph.add_argument('--path',

command_line/cadbiom_cmd/interaction_graph.py

@@ -99,10 +99,10 @@ def get_solutions_and_related_places_from_file(file_path):
 
         yield (
             tuple(solution['solution'].split(' ')),
-            set(it.chain(*((transition['ext'],transition['ori'])
-                for step in solution['steps']
-                for event in step
-                for transition in event['transitions']))))
+            set(it.chain(*((transition['ext'], transition['ori'])
+                           for step in solution['steps']
+                           for event in step
+                           for transition in event['transitions']))))
 
 
 def get_solutions_and_related_places(path):
@@ -152,9 +152,6 @@ def filter_trajectories(trajectories, molecules_of_interest):
     """Get solutions and count frontier places related to the given molecules
     of interest.
 
-    binary_interactions: binary_interactions[searched_molec] += Counter(sol)
-    compteur avec pour clés les entités des solutions liées à 1 molec d'intéret et avec leurs occurences pour valeurs
-
     :param trajectories: A generator of tuples with tuple of frontier places as
         keys and set of places involved in transitions as values.
 
@@ -165,7 +162,8 @@ def filter_trajectories(trajectories, molecules_of_interest):
     :type trajectories: <generator <tuple <tuple>, <set>>>
     :type molecules_of_interest: <tuple>
     :return: A tuple of all solutions related to the molecules of interest,
-        and a dictionary of related frontier places.
+        and a dictionary of related frontier places and their occurences for
+        each molecule of interest.
 
         .. code-block:: python
 
@@ -357,10 +355,10 @@ def build_interactions(filtered_macs, binary_interactions):
         molecule_stimuli_interactions
 
 
-def build_graph(output_dir, all_genes, all_stimuli, unique_genes_interactions,
-                unique_stimulis_interactions,
-                unique_genes_stimuli_interactions,
-                unique_molecule_stimuli_interactions):
+def build_graph(output_dir, all_genes, all_stimuli, genes_interactions,
+                stimulis_interactions,
+                genes_stimuli_interactions,
+                molecule_stimuli_interactions):
     """Make an interaction weighted graph based on the search of molecules of interest
 
     :Edges:
@@ -407,13 +405,14 @@ def build_graph(output_dir, all_genes, all_stimuli, unique_genes_interactions,
     LOGGER.info("Building graph...")
 
     # Count all nodes
-    nodes_count = Counter(it.chain(*unique_genes_interactions.keys()))
-    nodes_count.update(it.chain(*unique_stimulis_interactions.keys()))
-    nodes_count.update(it.chain(*unique_genes_stimuli_interactions.keys()))
-    nodes_count.update(it.chain(*unique_molecule_stimuli_interactions.keys()))
+    nodes_count = Counter(it.chain(*genes_interactions.keys()))
+    nodes_count.update(it.chain(*stimulis_interactions.keys()))
+    nodes_count.update(it.chain(*genes_stimuli_interactions.keys()))
+    nodes_count.update(it.chain(*molecule_stimuli_interactions.keys()))
 
     # Make Graph ###############################################################
     def colormap(node):
+        """Get color assigned to the given node depending on its group"""
         if node in all_genes:
             return 'red'
         elif node in all_stimuli:
@@ -428,21 +427,23 @@ def build_graph(output_dir, all_genes, all_stimuli, unique_genes_interactions,
      for node, weight in nodes_count.iteritems()]
 
     def build_edge_data(edges):
+        """Build edge tuple for networkx API"""
         return [(node1, node2, weight) for (node1, node2), weight in edges.iteritems()]
 
     # Add all edges
     # PS Syntax: G.add_weighted_edges_from([(0,1,3.0),(1,2,7.5)],color='red')
     # Interactions between genes in the same solution
     G.add_weighted_edges_from(
-        build_edge_data(unique_genes_interactions), color='red')
+        build_edge_data(genes_interactions), color='red')
     # Interactions between stimuli in the same solution
-    #G.add_weighted_edges_from(build_edge_data(unique_stimulis_interactions), color='blue')
+    #G.add_weighted_edges_from(build_edge_data(stimulis_interactions), color='blue')
     # Interactions between genes and stimulis in the same solution
     G.add_weighted_edges_from(
-        build_edge_data(unique_genes_stimuli_interactions), color='red')
-    # Interactions between molecules of interest and frontier places that are not genes in trajectories
+        build_edge_data(genes_stimuli_interactions), color='red')
+    # Interactions between molecules of interest and frontier places
+    # that are not genes in trajectories
     G.add_weighted_edges_from(
-        build_edge_data(unique_molecule_stimuli_interactions), color='yellow')
+        build_edge_data(molecule_stimuli_interactions), color='yellow')
 
     # Write graph
     nx.write_graphml(G, output_dir + "interaction_graph.graphml")