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authorFrederick Muriuki Muriithi2024-02-05 12:11:43 +0300
committerFrederick Muriuki Muriithi2024-02-05 12:11:43 +0300
commit949ea71eb721a3f5bdff3ba10f7dd7c70899d560 (patch)
tree5ea0674953489ce83ffa11c2b689d3c8e31ebede /scripts/rqtl2
parentab71b34b97f3f1eee52b5688f41644541535f281 (diff)
downloadgn-uploader-949ea71eb721a3f5bdff3ba10f7dd7c70899d560.tar.gz
Fix linting and type errors.
Diffstat (limited to 'scripts/rqtl2')
-rw-r--r--scripts/rqtl2/install_genotypes.py3
-rw-r--r--scripts/rqtl2/install_phenos.py3
2 files changed, 4 insertions, 2 deletions
diff --git a/scripts/rqtl2/install_genotypes.py b/scripts/rqtl2/install_genotypes.py
index bfe17b8..7f3f65a 100644
--- a/scripts/rqtl2/install_genotypes.py
+++ b/scripts/rqtl2/install_genotypes.py
@@ -11,6 +11,7 @@ import MySQLdb as mdb
from MySQLdb.cursors import DictCursor
from r_qtl import r_qtl2 as rqtl2
+from r_qtl import r_qtl2_qc as rqc
from functional_tools import take
@@ -166,7 +167,7 @@ def install_genotypes(#pylint: disable=[too-many-arguments, too-many-locals]
with ZipFile(str(rqtl2bundle.absolute()), "r") as zfile:
try:
logger.info("Validating bundle")
- rqtl2.validate_bundle(zfile)
+ rqc.validate_bundle(zfile)
logger.info("Bundle validated successfully.")
logger.info(("Loading genotypes. This could take a while. "
"Please be patient."))
diff --git a/scripts/rqtl2/install_phenos.py b/scripts/rqtl2/install_phenos.py
index a6cdacc..95745d7 100644
--- a/scripts/rqtl2/install_phenos.py
+++ b/scripts/rqtl2/install_phenos.py
@@ -14,6 +14,7 @@ from scripts.rqtl2.cli_parser import add_common_arguments
from scripts.cli_parser import init_cli_parser, add_global_data_arguments
from r_qtl import r_qtl2 as rqtl2
+from r_qtl import r_qtl2_qc as rqc
from functional_tools import take
@@ -102,7 +103,7 @@ def install_pheno_files(#pylint: disable=[too-many-arguments, too-many-locals]
"""Load data in `pheno` files and other related files into the database."""
with ZipFile(str(rqtl2bundle), "r") as zfile:
try:
- rqtl2.validate_bundle(zfile)
+ rqc.validate_bundle(zfile)
logger.info("R/qtl2 bundle validated successfully.")
cdata = rqtl2.control_data(zfile)