From 55ea1762b493f4248c23c33e4d7af4e76fe73825 Mon Sep 17 00:00:00 2001
From: Fontrodona Nicolas <nicolas.fontrodona@ens-lyon.fr>
Date: Wed, 15 Jul 2020 15:53:58 +0200
Subject: [PATCH] move get_community from
src/find_interaction_cluster/community_finder.py to
src/find_interaction_cluster/config.py
---
.../community_finder.py | 23 ++-----------------
src/find_interaction_cluster/config.py | 20 ++++++++++++++++
2 files changed, 22 insertions(+), 21 deletions(-)
diff --git a/src/find_interaction_cluster/community_finder.py b/src/find_interaction_cluster/community_finder.py
index 82dfbf92..0ae68de0 100644
--- a/src/find_interaction_cluster/community_finder.py
+++ b/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 = {}
diff --git a/src/find_interaction_cluster/config.py b/src/find_interaction_cluster/config.py
index a35de055..0fbafd92 100644
--- a/src/find_interaction_cluster/config.py
+++ b/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
--
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