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Léo HENCHES
jass
Commits
831d369d
Commit
831d369d
authored
1 year ago
by
Hanna JULIENNE
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added optional parameter to the create inittable command line
parent
c10cf502
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jass/__main__.py
+18
-3
18 additions, 3 deletions
jass/__main__.py
jass/test/data_test1/initTable.hdf5
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-0
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jass/test/data_test1/initTable.hdf5
jass/test/data_test2/initTable.hdf5
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jass/test/data_test2/initTable.hdf5
with
18 additions
and
3 deletions
jass/__main__.py
+
18
−
3
View file @
831d369d
...
@@ -5,14 +5,14 @@ import os
...
@@ -5,14 +5,14 @@ import os
import
shutil
import
shutil
import
sys
import
sys
import
argparse
import
argparse
from
datetime
import
timedelta
,
datetime
from
datetime
import
timedelta
,
datetime
,
date
from
json
import
JSONDecodeError
from
json
import
JSONDecodeError
import
uvicorn
import
uvicorn
from
jass.config
import
config
from
jass.config
import
config
from
jass.models.phenotype
import
get_available_phenotypes
from
jass.models.phenotype
import
get_available_phenotypes
from
jass.models.inittable
import
create_inittable_file
,
add_gene_annotation
from
jass.models.inittable
import
create_inittable_file
,
add_gene_annotation
,
add_inittable_meta
from
jass.models.worktable
import
create_worktable_file
from
jass.models.worktable
import
create_worktable_file
from
jass.models.project
import
get_projects_last_access
,
load_project
from
jass.models.project
import
get_projects_last_access
,
load_project
from
jass.models.plots
import
(
from
jass.models.plots
import
(
...
@@ -241,7 +241,8 @@ def w_create_inittable(args):
...
@@ -241,7 +241,8 @@ def w_create_inittable(args):
init_covariance_path
,
init_covariance_path
,
init_genetic_covariance_path
,
init_genetic_covariance_path
,
)
)
add_inittable_meta
(
init_table_path
,
args
.
title
,
args
.
description_inittable
)
def
w_plot_manhattan
(
args
):
def
w_plot_manhattan
(
args
):
worktable_path
=
absolute_path_of_the_file
(
args
.
worktable_path
)
worktable_path
=
absolute_path_of_the_file
(
args
.
worktable_path
)
...
@@ -438,6 +439,20 @@ def get_parser():
...
@@ -438,6 +439,20 @@ def get_parser():
default
=
None
,
default
=
None
,
help
=
"
path to the genetic covariance file to import. Used only for display on Jass web application
"
,
help
=
"
path to the genetic covariance file to import. Used only for display on Jass web application
"
,
)
)
parser_create_it
.
add_argument
(
"
--title
"
,
required
=
False
,
default
=
"
inittable_{}
"
.
format
(
date
.
today
()),
help
=
"
Title of the dataset (optional)
"
,
)
parser_create_it
.
add_argument
(
"
--description-inittable
"
,
required
=
False
,
default
=
"
inittable generated the {}
"
.
format
(
date
.
today
()),
help
=
"
Textual description of the dataset (optional)
"
,
)
parser_create_it
.
set_defaults
(
func
=
w_create_inittable
)
parser_create_it
.
set_defaults
(
func
=
w_create_inittable
)
# ------- create-worktable -------
# ------- create-worktable -------
...
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