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authorFrederick Muriuki Muriithi2024-10-17 14:18:22 -0500
committerFrederick Muriuki Muriithi2024-10-17 14:39:42 -0500
commit0f434659f79da67d3d440c5fb0cb9ea8a1ec5cbd (patch)
treea74a377d96e938ce113e21f393aebef725284ad2 /scripts/rqtl2
parentdb196d5ea2dd2ffbb6d9ff4b9fcc5dd2b2d66678 (diff)
downloadgn-uploader-0f434659f79da67d3d440c5fb0cb9ea8a1ec5cbd.tar.gz
Add `speciesid` and `populationid` arguments to the script.
Diffstat (limited to 'scripts/rqtl2')
-rw-r--r--scripts/rqtl2/phenotypes_qc.py7
1 files changed, 3 insertions, 4 deletions
diff --git a/scripts/rqtl2/phenotypes_qc.py b/scripts/rqtl2/phenotypes_qc.py
index 9d58137..f602681 100644
--- a/scripts/rqtl2/phenotypes_qc.py
+++ b/scripts/rqtl2/phenotypes_qc.py
@@ -2,7 +2,6 @@
import sys
import tempfile
from pathlib import Path
-from argparse import ArgumentParser
from zipfile import ZipFile
from logging import Logger, getLogger, StreamHandler
@@ -12,10 +11,10 @@ from r_qtl import r_qtl2 as rqtl2
from r_qtl import r_qtl2_qc as rqc
from r_qtl import exceptions as rqe
-from scripts.cli_parser import init_cli_parser
from uploader.files import sha256_digest_over_file
from scripts.rqtl2.entry import build_main
from scripts.rqtl2.cli_parser import add_bundle_argument
+from scripts.cli_parser import init_cli_parser, add_global_data_arguments
def validate(phenobundle: Path, logger: Logger) -> dict:
"""Check that the bundle is generally valid"""
@@ -125,10 +124,10 @@ if __name__ == "__main__":
def cli_args():
"""Process command-line arguments for `install_phenos`"""
- parser = add_bundle_argument(init_cli_parser(
+ parser = add_bundle_argument(add_global_data_arguments(init_cli_parser(
program="PhenotypesQC",
description=(
- "Perform Quality Control checks on a phenotypes bundle file")))
+ "Perform Quality Control checks on a phenotypes bundle file"))))
parser.add_argument(
"--working-dir",
default=f"{tempfile.gettempdir()}/phenotypes_qc",