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Statistical-Genetics
RAISS
Commits
a889f9c2
Commit
a889f9c2
authored
Mar 29, 2018
by
Hanna JULIENNE
Browse files
fix commit
parent
62fee36f
Changes
1
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Side-by-side
impute_jass/impute_jass/__main__.py
View file @
a889f9c2
...
@@ -14,14 +14,14 @@ def launch_chromosome_imputation(args):
...
@@ -14,14 +14,14 @@ def launch_chromosome_imputation(args):
z_file
=
"{0}/z_{1}_{2}.txt"
.
format
(
args
.
zscore_folder
,
args
.
gwas
,
args
.
chrom
)
z_file
=
"{0}/z_{1}_{2}.txt"
.
format
(
args
.
zscore_folder
,
args
.
gwas
,
args
.
chrom
)
zscore
=
pd
.
read_csv
(
z_file
)
zscore
=
pd
.
read_csv
(
z_file
)
imputer
.
chromosome_imputation
(
args
.
chrom
,
zscore
,
ref_panel
,
ld_folder
)
imputer
.
chromosome_imputation
(
args
.
chrom
,
zscore
,
args
.
ref_panel
,
args
.
ld_folder
)
def
add_chromosome_imputation_argument
(
parser
):
def
add_chromosome_imputation_argument
(
parser
):
parser
.
add_argument
(
'--chrom'
,
required
=
True
,
help
=
"chromosome to impute to the chr\d+ format"
)
parser
.
add_argument
(
'--chrom'
,
required
=
True
,
help
=
"chromosome to impute to the chr\d+ format"
)
parser
.
add_argument
(
'--gwas'
,
required
=
True
,
help
=
"GWAS to impute to the consortia_trait format"
)
parser
.
add_argument
(
'--gwas'
,
required
=
True
,
help
=
"GWAS to impute to the consortia_trait format"
)
parser
.
add_argument
(
'--ref-folder'
,
required
=
True
,
help
=
"reference panel location (used to determine which snp to impute)"
)
parser
.
add_argument
(
'--ref-folder'
,
required
=
True
,
help
=
"reference panel location (used to determine which snp to impute)"
)
parser
.
add_argument
(
'--
LD
-folder'
,
required
=
True
,
help
=
"Location LD correlation matrices"
)
parser
.
add_argument
(
'--
ld
-folder'
,
required
=
True
,
help
=
"Location LD correlation matrices"
)
parser
.
add_argument
(
'--zscore-folder'
,
required
=
True
,
help
=
"Location of the zscore files of the gwases to impute"
)
parser
.
add_argument
(
'--zscore-folder'
,
required
=
True
,
help
=
"Location of the zscore files of the gwases to impute"
)
parser
.
add_argument
(
'--output-folder'
,
required
=
True
,
help
=
"Location of the impute zscore files"
)
parser
.
add_argument
(
'--output-folder'
,
required
=
True
,
help
=
"Location of the impute zscore files"
)
...
...
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