From 9cc3eb53d7ca43eed80aa2f13ca01ef6ede15368 Mon Sep 17 00:00:00 2001
From: Fontrodona Nicolas <nicolas.fontrodona@ens-lyon.fr>
Date: Fri, 10 Jul 2020 10:12:20 +0200
Subject: [PATCH] src/find_interaction_cluster/config.py: chnage cpu value
---
src/find_interaction_cluster/config.py | 33 +++++++++++++++++++++++---
1 file changed, 30 insertions(+), 3 deletions(-)
diff --git a/src/find_interaction_cluster/config.py b/src/find_interaction_cluster/config.py
index 58ed8283..0cbd7d15 100644
--- a/src/find_interaction_cluster/config.py
+++ b/src/find_interaction_cluster/config.py
@@ -10,8 +10,31 @@ from ..db_utils.config import Config
from pathlib import Path
+def get_weight_folder(weight: int, global_weight: int):
+ """
+ Get the weight folder.
+
+ :param weight: The weight of interaction to consider
+ :param global_weight: The global weight to consider. if \
+ the global weight is equal to 0 then then density figure are calculated \
+ by project, else all projet are merge together and the interaction \
+ seen in `global_weight` project are taken into account
+ :return: The folder that will contains the interaction with a weight \
+ greater or equal to `weigh` in ChIA-PET projects
+ """
+ if global_weight == 0:
+ weight_folder = ConfigGraph.community_folder / \
+ f"project_weight-{weight}"
+ else:
+ weight_folder = ConfigGraph.community_folder / \
+ f"weight-{weight}_" \
+ f"global_weight-{global_weight}"
+ weight_folder.mkdir(parents=True, exist_ok=True)
+ return weight_folder
+
+
def get_community_file(project: str, weight: int, global_weight: int,
- same_gene: bool, ext: str = ".txt"):
+ same_gene: bool, ext: str = ".txt", stat: bool = False):
"""
Get the output file of interest.
@@ -24,9 +47,13 @@ def get_community_file(project: str, weight: int, global_weight: int,
:param same_gene: Say if we consider as co-localised exon within the \
same gene
:param ext: The file extension
+ :param stat: True to place the result in 'sf_community_enrichment' \
+ subfolder
:return: The filename of interest
"""
- folder = ConfigGraph.community_folder
+ folder = get_weight_folder(weight, global_weight)
+ if stat:
+ folder = folder / 'sf_community_enrichment'
folder.mkdir(exist_ok=True, parents=True)
if global_weight != 0:
project = f"global-weight-{global_weight}"
@@ -55,7 +82,7 @@ class ConfigGraph:
Class containing all the variables that will be used in this submodule
"""
data = Config.data
- cpu = 1 # Config.cpu
+ cpu = 7 # Config.cpu
db_file = Config.db_file
results = Config.results
output_folder = results / 'community_of_co-localized-exons'
--
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