From 58f72dd347f9c639f36387777819a01a9e6d8e78 Mon Sep 17 00:00:00 2001
From: hanna julienne <hanna.julienne@pasteur.fr>
Date: Tue, 29 Oct 2019 17:02:58 +0100
Subject: [PATCH] fixed main
---
jass/__main__.py | 18 +++++++++++-------
1 file changed, 11 insertions(+), 7 deletions(-)
diff --git a/jass/__main__.py b/jass/__main__.py
index dba98327..551bd539 100644
--- a/jass/__main__.py
+++ b/jass/__main__.py
@@ -25,7 +25,7 @@ def compute_worktable(args):
selected_phenotypes = args.phenotypes
worktable_path = args.worktable_path
remove_nan = not (args.keep_nans)
- significance_treshold = args.significance_treshold
+ significance_treshold = float(args.significance_treshold)
post_filtering = args.post_filtering
custom_loadings=args.custom_loadings
@@ -48,8 +48,11 @@ def w_create_worktable(args):
def w_create_project_data(args):
compute_worktable(args)
+ worktable_path = args.worktable_path
+ manhattan_plot_path = args.manhattan_plot_path
+ quadrant_plot_path = args.quadrant_plot_path
create_global_plot(worktable_path, manhattan_plot_path)
- create_quadrant_plot(worktable_path, quadrant_plot_path, significance_treshold = significance_treshold)
+ create_quadrant_plot(worktable_path, quadrant_plot_path, significance_treshold = float(args.significance_treshold))
def w_create_inittable(args):
@@ -66,11 +69,6 @@ def w_create_inittable(args):
init_table_path,
)
-
-
-
-
-
def w_plot_manhattan(args):
worktable_path = args.worktable_path
plot_path = args.plot_path
@@ -208,6 +206,12 @@ def get_parser():
default=True,
help="If a filtering to remove outlier will be applied (in this case the result of SNPs considered aberant will not appear in the worktable)"
)
+
+ parser_create_wt.add_argument(
+ "--custom-loadings",
+ required=False,
+ help="path toward a csv file containing custom loading for sumZ tests",
+ )
parser_create_wt.add_argument("--keep-nans", action="store_true", default=False)
strategies = parser_create_wt.add_mutually_exclusive_group()
strategies.add_argument("--omnibus", action="store_true", default=True)
--
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