src/find_interaction_cluster/community_finder.py: fix create_graph to use...

src/find_interaction_cluster/community_finder.py: fix create_graph to use weight if wanted + add 2 paramters in findo_community functions

src/find_interaction_cluster/community_finder.py

@@ -49,7 +49,7 @@ def create_graph(interaction: np.array) -> nx.Graph:
     graph = nx.Graph()
     graph.add_nodes_from(nodes)
     for inter in interaction:
-        graph.add_edge(inter[0], inter[1], weight=inter[2])
+        graph.add_edge(inter[0], inter[1], weight=float(inter[2]))
     logging.debug(f'Node : {len(nodes)} - Edges : {len(interaction)}')
     return graph
 
@@ -87,7 +87,8 @@ def write_cytoscape_graph(graph: nx.Graph, dic_community: Dict[str, str],
 
 def find_communities(graph: nx.Graph, project: str,
                      outfile: Path, result_file: Path,
-                     feature: str = 'exon') -> Tuple[pd.DataFrame, Dict]:
+                     feature: str = 'exon', inflation: float = 1.5,
+                     compute_ec_cov: bool = True) -> Tuple[pd.DataFrame, Dict]:
     """
     Find the communities within the graph.
 
@@ -95,6 +96,9 @@ def find_communities(graph: nx.Graph, project: str,
     :param project: The name of the project
     :param outfile: A file containing interaction
     :param feature: the kind of analysed feature (exons or gene)
+    :param inflation: The inflation parameter
+    :param compute_ec_cov: If true, compute edges connectivity and \
+    coverage.
     :return: The communities within the graph and the community \
     to wich each exon belong
     """
@@ -102,12 +106,14 @@ def find_communities(graph: nx.Graph, project: str,
     logging.debug("Finding community ...")
     if not result_file.is_file():
         cmd = f"mpirun -np 1 {ConfigGraph.get_hipmcl_prog()} -M {outfile} " \
-              f"-I 1.5 -per-process-mem 50 -o {result_file}"
+              f"-I {inflation} -per-process-mem 50 -o {result_file}"
         sp.check_call(cmd, shell=True, stderr=sp.STDOUT)
     communities = get_communities_basefile(result_file)
     dic_community = {}
-    cov = round(community.coverage(graph, communities), 2)
-    modularity = community.modularity(graph, communities, weight='X')
+    cov = np.nan
+    if compute_ec_cov:
+        cov = round(community.coverage(graph, communities), 2)
+    modularity = community.modularity(graph, communities, weight='weight')
     d = {'community': [], 'nodes': [], 'edges': [], 'EC': [], 'HCS': [],
          '%E vs E in complete G': [],
          'cov': [], 'modularity': [], f'{feature}s': []}
@@ -124,7 +130,9 @@ def find_communities(graph: nx.Graph, project: str,
                              2)
         except ZeroDivisionError:
             complete = np.nan
-        edge_connectivity = nx.edge_connectivity(subg)
+        edge_connectivity = np.nan
+        if compute_ec_cov:
+            edge_connectivity = nx.edge_connectivity(subg)
         is_hc = 'yes' if edge_connectivity > nb_nodes / 2 else 'no'
         for exon in c:
             dic_community[exon] = {'num': f'C{k + 1}',