From 919ab7a956a00fc6464c3b0b93dbea5a646c3a04 Mon Sep 17 00:00:00 2001
From: Fontrodona Nicolas <nicolas.fontrodona@ens-lyon.fr>
Date: Tue, 4 Aug 2020 14:52:29 +0200
Subject: [PATCH] src/db_utils/populate_database.py: refactoring of 2 lines
---
src/db_utils/populate_database.py | 8 ++------
src/find_interaction_cluster/__main__.py | 4 ++--
2 files changed, 4 insertions(+), 8 deletions(-)
diff --git a/src/db_utils/populate_database.py b/src/db_utils/populate_database.py
index 4fcf80ff..68d43243 100755
--- a/src/db_utils/populate_database.py
+++ b/src/db_utils/populate_database.py
@@ -43,8 +43,7 @@ def get_number_columns(table: str, cnx: sqlite3.Connection) -> List[str]:
cursor.execute(query)
cols_data = cursor.fetchall()
cursor.close()
- col_name = [col[1] for col in cols_data]
- return col_name
+ return [col[1] for col in cols_data]
def check_file(table: str, file: Union[Path, pd.DataFrame],
@@ -61,10 +60,7 @@ def check_file(table: str, file: Union[Path, pd.DataFrame],
:return: The row in file.
"""
column_names = get_number_columns(table, cnx)
- if isinstance(file, Path):
- df = pd.read_csv(file, sep="\t")
- else:
- df = file
+ df = pd.read_csv(file, sep="\t") if isinstance(file, Path) else file
if len(df.columns) != len(column_names):
msg = "Wrong number of columns"
logging.exception(msg)
diff --git a/src/find_interaction_cluster/__main__.py b/src/find_interaction_cluster/__main__.py
index 184339c9..bbe8de7d 100644
--- a/src/find_interaction_cluster/__main__.py
+++ b/src/find_interaction_cluster/__main__.py
@@ -38,8 +38,8 @@ def launcher(weight: List[int] = (1),
"""
if not ConfigGraph.get_hipmcl_prog().is_file():
install_hipmcl("INFO")
- multiple_community_launcher(1, weight, global_weight, same_gene, html_fig,
- logging_level)
+ # multiple_community_launcher(1, weight, global_weight, same_gene, html_fig,
+ # logging_level)
multiple_stat_launcher(ps, weight, global_weight, same_gene,
logging_level)
--
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