From 3ccf6dac48773952e2ac6c49c90debd6e141a268 Mon Sep 17 00:00:00 2001
From: hjulienn <hanna.julienne@pasteur.fr>
Date: Wed, 30 Nov 2022 15:02:21 +0100
Subject: [PATCH] float for sample size filter argument
---
jass_preprocessing/__main__.py | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/jass_preprocessing/__main__.py b/jass_preprocessing/__main__.py
index 30d6985..9ef13c5 100644
--- a/jass_preprocessing/__main__.py
+++ b/jass_preprocessing/__main__.py
@@ -62,9 +62,9 @@ def launch_preprocessing(args):
print("#SNPs mapped to reference panel: {}".format(mgwas.shape[0]))
mgwas = jp.map_reference.compute_snp_alignement(mgwas)
mgwas = jp.compute_score.compute_z_score(mgwas)
- mgwas = jp.compute_score.compute_sample_size(mgwas, args.diagnostic_folder, tag, args.percent_sample_size)
+ mgwas = jp.compute_score.compute_sample_size(mgwas, args.diagnostic_folder, tag, float(args.percent_sample_size))
end = time.time()
-
+
print("#SNPs remaining after sample size filter: {}".format(mgwas.shape[0]))
print("Preprocessing of {0} in {1}s".format(tag, end-start))
jp.save_output.save_output_by_chromosome(mgwas, args.output_folder, tag)
--
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