From 9dc76727b6c69b7bec39a07af84f0e7def0374e4 Mon Sep 17 00:00:00 2001
From: Hanna JULIENNE <hanna.julienne@pasteur.fr>
Date: Wed, 9 Jun 2021 19:05:47 +0200
Subject: [PATCH] change the --keep-nans argument to --remove-nans to change
defaults behaviour
---
jass/__main__.py | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/jass/__main__.py b/jass/__main__.py
index 27b0e25e..743b2905 100644
--- a/jass/__main__.py
+++ b/jass/__main__.py
@@ -79,7 +79,7 @@ def compute_worktable(args):
init_table_path = absolute_path_of_the_file(args.init_table_path)
worktable_path = absolute_path_of_the_file(args.worktable_path, True)
selected_phenotypes = args.phenotypes
- remove_nan = not (args.keep_nans)
+ remove_nan = (args.remove_nans)
significance_treshold = float(args.significance_treshold)
post_filtering = bool(args.post_filtering)
custom_loadings = args.custom_loadings
@@ -197,7 +197,7 @@ def get_parser():
parser_create_pd.add_argument(
"--worktable-path", required=True, help="path to the worktable file to generate"
)
- parser_create_pd.add_argument("--keep-nans", action="store_true", default=True)
+ parser_create_pd.add_argument("--remove-nans", action="store_true", default=False)
parser_create_pd.add_argument(
"--manhattan-plot-path",
required=True,
@@ -344,7 +344,7 @@ def get_parser():
help="Number of region to load in memory at once",
)
- parser_create_wt.add_argument("--keep-nans", action="store_true", default=True)
+ parser_create_wt.add_argument("--remove-nans", action="store_true", default=False)
parser_create_wt.add_argument(
"--chromosome-number",
--
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