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Statistical-Genetics
jass_preprocessing
Commits
9c12fe0a
Commit
9c12fe0a
authored
Dec 08, 2020
by
hjulienne
Browse files
precise type when reading reference
parent
51b18794
Pipeline
#42969
passed with stages
in 57 seconds
Changes
1
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1
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Inline
Side-by-side
jass_preprocessing/map_reference.py
View file @
9c12fe0a
...
...
@@ -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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