move get_community from src/find_interaction_cluster/community_finder.py to...

move get_community from src/find_interaction_cluster/community_finder.py to src/find_interaction_cluster/config.py

src/find_interaction_cluster/community_finder.py

@@ -11,7 +11,7 @@ import networkx as nx
 import numpy as np
 from networkx.algorithms import community
 import sqlite3
-from .config import ConfigGraph
+from .config import ConfigGraph, get_communities
 from ..nt_composition.make_nt_correlation import get_project_colocalisation
 from ..logging_conf import logging_def
 import pandas as pd
@@ -87,25 +87,6 @@ def write_cytoscape_graph(graph: nx.Graph, dic_community: Dict[str, str],
         f.write(res)
 
 
-def get_communities(result: Path, threshold: int = 0) -> List[List[str]]:
-    """
-    Get the communities inside the file `result`
-
-    :param result: A file containing the communities found by the hipMCL \
-    program.
-    :param threshold: The number of exon the community must contains at least \
-    to be recovered
-    :return: The list of communities find by the hipMCL program.
-    """
-    communities = []
-    with result.open('r') as f:
-        for line in f:
-            tmp = line.replace('\n', '').strip().split(' ')
-            if len(tmp) > threshold:
-                communities.append(tmp)
-    return communities
-
-
 def find_communities(graph: nx.Graph, project: str,
                      outfile: Path, result_file: Path
                      ) -> Tuple[pd.DataFrame, Dict]:
@@ -122,7 +103,7 @@ 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 1.2 -per-process-mem 50 -o {result_file}"
+              f"-I 1.5 -per-process-mem 50 -o {result_file}"
         sp.check_call(cmd, shell=True, stderr=sp.STDOUT)
     communities = get_communities(result_file)
     dic_community = {}

src/find_interaction_cluster/config.py

@@ -9,6 +9,7 @@ Description: Configuration folder
 from ..db_utils.config import Config
 from pathlib import Path
 from ..figures_utils.config_figures import get_good_project
+from typing import List
 
 
 def get_weight_folder(weight: int, global_weight: int):
@@ -78,6 +79,25 @@ def get_hipmcl_prog() -> Path:
     return get_hipmcl_folder() / "bin" / "hipmcl"
 
 
+def get_communities(result: Path, threshold: int = 0) -> List[List[str]]:
+    """
+    Get the communities inside the file `result`
+
+    :param result: A file containing the communities found by the hipMCL \
+    program.
+    :param threshold: The number of exon the community must contains at least \
+    to be recovered
+    :return: The list of communities find by the hipMCL program.
+    """
+    communities = []
+    with result.open('r') as f:
+        for line in f:
+            tmp = line.replace('\n', '').strip().split(' ')
+            if len(tmp) > threshold:
+                communities.append(tmp)
+    return communities
+
+
 class ConfigGraph:
     """
     Class containing all the variables that will be used in this submodule