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| author | Frederick Muriuki Muriithi | 2024-02-05 12:11:43 +0300 |
|---|---|---|
| committer | Frederick Muriuki Muriithi | 2024-02-05 12:11:43 +0300 |
| commit | 949ea71eb721a3f5bdff3ba10f7dd7c70899d560 (patch) | |
| tree | 5ea0674953489ce83ffa11c2b689d3c8e31ebede /scripts | |
| parent | ab71b34b97f3f1eee52b5688f41644541535f281 (diff) | |
| download | gn-uploader-949ea71eb721a3f5bdff3ba10f7dd7c70899d560.tar.gz | |
Fix linting and type errors.
Diffstat (limited to 'scripts')
| -rw-r--r-- | scripts/rqtl2/install_genotypes.py | 3 | ||||
| -rw-r--r-- | scripts/rqtl2/install_phenos.py | 3 |
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) |