From 9c12fe0a63254e6c18dba437165fc197c738975c Mon Sep 17 00:00:00 2001
From: hjulienne <hanna.julienne@gmail.com>
Date: Tue, 8 Dec 2020 17:35:13 +0100
Subject: [PATCH] precise type when reading reference
---
jass_preprocessing/map_reference.py | 1 +
1 file changed, 1 insertion(+)
diff --git a/jass_preprocessing/map_reference.py b/jass_preprocessing/map_reference.py
index 4a1be77..2edef8d 100644
--- a/jass_preprocessing/map_reference.py
+++ b/jass_preprocessing/map_reference.py
@@ -21,6 +21,7 @@ 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.float, "pos":np.int, "ref":str, "alt":str},
index_col="snp_id")
def sorted_alleles(x):
--
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