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Statistical-Genetics
jass_preprocessing
Commits
b0380f32
Commit
b0380f32
authored
Dec 08, 2020
by
hjulienne
Browse files
add debug print
parent
9c12fe0a
Pipeline
#42974
passed with stages
in 1 minute
Changes
2
Pipelines
1
Hide whitespace changes
Inline
Side-by-side
jass_preprocessing/__main__.py
View file @
b0380f32
...
...
@@ -59,7 +59,9 @@ def launch_preprocessing(args):
ref
=
jp
.
map_reference
.
read_reference
(
args
.
ref_path
,
bool
(
args
.
mask_MHC
),
float
(
args
.
minimum_MAF
),
region_to_mask
=
eval
(
args
.
additional_masked_region
))
print
(
ref
.
shape
)
print
(
ref
.
head
())
print
(
gw_df
.
shape
)
print
(
gw_df
.
head
())
mgwas
=
jp
.
map_reference
.
map_on_ref_panel
(
gw_df
,
ref
,
gwas_map
.
loc
[
tag
,
"index_type"
])
print
(
mgwas
.
shape
)
mgwas
=
jp
.
map_reference
.
compute_snp_alignement
(
mgwas
)
...
...
jass_preprocessing/map_gwas.py
View file @
b0380f32
...
...
@@ -134,7 +134,7 @@ def read_gwas( gwas_internal_link, column_map, imputation_treshold=None):
print
(
"Reading file:"
)
print
(
gwas_internal_link
)
is_gzipped
=
re
.
search
(
r
".gz$"
,
gwas_internal_link
)
is_gzipped
=
re
.
search
(
r
".gz
|.bgz
$"
,
gwas_internal_link
)
if
is_gzipped
:
compression
=
'gzip'
...
...
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