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Statistical-Genetics
jass_preprocessing
Commits
48a615de
Commit
48a615de
authored
Nov 29, 2018
by
Hanna JULIENNE
Browse files
cast command line args
parent
2533e552
Pipeline
#7903
passed with stages
in 1 minute and 27 seconds
Changes
2
Pipelines
1
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Inline
Side-by-side
jass_preprocessing/__main__.py
View file @
48a615de
...
...
@@ -36,7 +36,6 @@ def launch_preprocessing(args):
start
=
time
.
time
()
GWAS_link
=
jp
.
map_gwas
.
walkfs
(
args
.
gwas_folder
,
args
.
gwas_filename
)[
2
]
mapgw
=
jp
.
map_gwas
.
map_columns_position
(
GWAS_link
,
args
.
gwas_info
)
print
(
mapgw
)
gw_df
=
jp
.
map_gwas
.
read_gwas
(
GWAS_link
,
mapgw
)
...
...
jass_preprocessing/compute_score.py
View file @
48a615de
...
...
@@ -51,7 +51,7 @@ def compute_sample_size(mgwas, diagnostic_folder, trait, perSS = 0.7):
warnings
.
warn
(
"Some snp had an infinite sample size"
)
myW_thres
=
np
.
percentile
(
myN
.
dropna
(),
90
)
ss_thres
=
perSS
*
myW_thres
ss_thres
=
int
(
perSS
)
*
myW_thres
mgwas
[
"computed_N"
]
=
myN
plt
.
clf
()
p1
=
sns
.
distplot
(
mgwas
.
computed_N
[
~
mgwas
.
computed_N
.
isna
()])
...
...
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