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Statistical-Genetics
jass_preprocessing
Commits
fd935ad8
Commit
fd935ad8
authored
Jul 19, 2021
by
Hanna JULIENNE
Browse files
Update save_output.py
parent
334f61a0
Pipeline
#61488
failed with stage
in 24 seconds
Changes
1
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1
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Inline
Side-by-side
jass_preprocessing/save_output.py
View file @
fd935ad8
...
...
@@ -12,19 +12,22 @@ def save_output_by_chromosome(mgwas, ImpG_output_Folder, my_study):
mgwas_copy
.
dropna
(
subset
=
[
"computed_z"
],
how
=
"any"
,
inplace
=
True
)
print
(
mgwas_copy
.
index
.
unique
())
for
chrom
in
mgwas_copy
.
index
.
unique
():
print
(
mgwas_copy
.
loc
[
chrom
])
mgwas_chr
=
pd
.
DataFrame
({
'rsID'
:
mgwas_copy
.
loc
[
chrom
].
snp_id
,
'pos'
:
mgwas_copy
.
loc
[
chrom
].
pos
,
'A0'
:
mgwas_copy
.
loc
[
chrom
].
ref
,
'A1'
:
mgwas_copy
.
loc
[
chrom
].
alt
,
'Z'
:
mgwas_copy
.
loc
[
chrom
].
computed_z
,
'P'
:
mgwas_copy
.
loc
[
chrom
].
pval
},
columns
=
[
'rsID'
,
'pos'
,
'A0'
,
"A1"
,
"Z"
,
"P"
])
impg_output_file
=
ImpG_output_Folder
+
'z_'
+
my_study
+
'_chr'
+
str
(
chrom
)
+
".txt"
print
(
"WRITING CHR {} results for {} to: {}"
.
format
(
chrom
,
my_study
,
ImpG_output_Folder
))
mgwas_chr
.
sort_values
(
by
=
"pos"
).
to_csv
(
impg_output_file
,
sep
=
"
\t
"
,
index
=
False
)
if
type
(
mgwas_copy
.
loc
[
chrom
])
is
pd
.
core
.
frame
.
DataFrame
:
print
(
mgwas_copy
.
loc
[
chrom
])
mgwas_chr
=
pd
.
DataFrame
({
'rsID'
:
mgwas_copy
.
loc
[
chrom
].
snp_id
,
'pos'
:
mgwas_copy
.
loc
[
chrom
].
pos
,
'A0'
:
mgwas_copy
.
loc
[
chrom
].
ref
,
'A1'
:
mgwas_copy
.
loc
[
chrom
].
alt
,
'Z'
:
mgwas_copy
.
loc
[
chrom
].
computed_z
,
'P'
:
mgwas_copy
.
loc
[
chrom
].
pval
},
columns
=
[
'rsID'
,
'pos'
,
'A0'
,
"A1"
,
"Z"
,
"P"
])
impg_output_file
=
ImpG_output_Folder
+
'z_'
+
my_study
+
'_chr'
+
str
(
chrom
)
+
".txt"
print
(
"WRITING CHR {} results for {} to: {}"
.
format
(
chrom
,
my_study
,
ImpG_output_Folder
))
mgwas_chr
.
sort_values
(
by
=
"pos"
).
to_csv
(
impg_output_file
,
sep
=
"
\t
"
,
index
=
False
)
else
:
print
(
"NO or 1 value for CHR {} results for {} to: {}"
.
format
(
chrom
,
my_study
,
ImpG_output_Folder
))
def
save_output
(
mgwas
,
ImpG_output_Folder
,
my_study
):
...
...
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