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Statistical-Genetics
jass_preprocessing
Commits
823976b5
Commit
823976b5
authored
Nov 18, 2019
by
Hanna JULIENNE
Browse files
corrected column mix up when snpid is not first
parent
b8b082b3
Pipeline
#18396
passed with stages
in 51 seconds
Changes
1
Pipelines
1
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Inline
Side-by-side
jass_preprocessing/map_gwas.py
View file @
823976b5
...
...
@@ -152,13 +152,13 @@ def read_gwas( gwas_internal_link, column_map):
compression
=
compression
,
#column_dict['label_position'].keys(),
names
=
column_map
.
index
,
index_col
=
0
,
header
=
0
,
na_values
=
[
''
,
'#N/A'
,
'#N/A'
,
'N/A'
,
'#NA'
,
'-1.#IND'
,
'-1.#QNAN'
,
'-NaN'
,
'-nan'
,
'1.#IND'
,
'1.#QNAN'
,
'N/A'
,
'NA'
,
'NULL'
,
'NaN'
,
'nan'
,
'na'
,
'.'
])
'nan'
,
'na'
,
'.'
,
'-'
],
dtype
=
{
"snpid"
:
str
,
"a1"
:
str
,
"a2"
:
str
,
"freq"
:
float
,
"z"
:
float
,
"se"
:
float
,
"pval"
:
float
})
print
(
fullGWAS
.
head
())
fullGWAS
.
set_index
(
"snpid"
,
inplace
=
True
)
print
(
fullGWAS
.
head
())
fullGWAS
=
fullGWAS
[
~
fullGWAS
.
index
.
duplicated
(
keep
=
'first'
)]
#fullGWAS = convert_missing_values(fullGWAS)
...
...
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