From 437be19699ae1a3c7ce22908dca4b036f6c7a4b6 Mon Sep 17 00:00:00 2001
From: hjulienn <hanna.julienne@pasteur.fr>
Date: Thu, 5 Jan 2023 13:20:52 +0100
Subject: [PATCH] treat exception when missing position
---
jass_preprocessing/map_reference.py | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/jass_preprocessing/map_reference.py b/jass_preprocessing/map_reference.py
index 65550fd..260e16e 100644
--- a/jass_preprocessing/map_reference.py
+++ b/jass_preprocessing/map_reference.py
@@ -21,8 +21,10 @@ def read_reference(gwas_reference_panel, mask_MHC=False, minimum_MAF=None, regio
"""
ref = pd.read_csv(gwas_reference_panel, header=None, sep= "\t",
names =[ 'chr', "snp_id", "MAF","pos", "ref", "alt"],
- dtype = {"chr": str, "snp_id":str, "MAF": np.double, "pos":np.int64, "ref":str, "alt":str},
+ dtype = {"chr": str, "snp_id":str, "MAF": np.double, "pos":np.double, "ref":str, "alt":str},
index_col="snp_id")
+ ref = ref.loc[~ref.pos.isnull()]
+ ref.pos = ref.pos.astype('int')
def sorted_alleles(x):
return "".join(sorted(x))
--
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