From cf1f8a3b6983d6877227b08340455d97feaa7ceb Mon Sep 17 00:00:00 2001
From: Fontrodona Nicolas <nicolas.fontrodona@ens-lyon.fr>
Date: Mon, 6 Jul 2020 16:00:25 +0200
Subject: [PATCH] src/find_interaction_cluster/config.py: creation of three new
variables get_hip_folder, get_hipmcl_prog and hip_zip
---
src/find_interaction_cluster/config.py | 26 +++++++++++++++++++++++---
1 file changed, 23 insertions(+), 3 deletions(-)
diff --git a/src/find_interaction_cluster/config.py b/src/find_interaction_cluster/config.py
index 2106604a..58ed8283 100644
--- a/src/find_interaction_cluster/config.py
+++ b/src/find_interaction_cluster/config.py
@@ -7,6 +7,7 @@ Description: Configuration folder
"""
from ..db_utils.config import Config
+from pathlib import Path
def get_community_file(project: str, weight: int, global_weight: int,
@@ -27,21 +28,40 @@ def get_community_file(project: str, weight: int, global_weight: int,
"""
folder = ConfigGraph.community_folder
folder.mkdir(exist_ok=True, parents=True)
- if ext[0] != '.':
- ext = "." + ext
if global_weight != 0:
project = f"global-weight-{global_weight}"
return folder / f"{project}_weight-{weight}_same_gene-{same_gene}{ext}"
+def get_hipmcl_folder() -> Path:
+ """
+ Return the name of the hipmlc folder
+ :return: The hipmlc folder
+ """
+ return list(Config.data.glob('*hipmcl*'))[0]
+
+
+def get_hipmcl_prog() -> Path:
+ """
+ Get the hipmcl program.
+
+ :return: The file corresponding to hipmcl program
+ """
+ return get_hipmcl_folder() / "bin" / "hipmcl"
+
+
class ConfigGraph:
"""
Class containing all the variables that will be used in this submodule
"""
data = Config.data
- cpu = Config.cpu
+ cpu = 1 #Â Config.cpu
db_file = Config.db_file
results = Config.results
output_folder = results / 'community_of_co-localized-exons'
community_folder = output_folder / 'communities'
get_community_file = get_community_file
+ hip_zip = data / 'hipMCL.zip'
+ get_hip_folder = get_hipmcl_folder
+ get_hipmcl_prog = get_hipmcl_prog
+
--
GitLab