diff options
Diffstat (limited to 'scripts/process_rqtl2_bundle.py')
| -rw-r--r-- | scripts/process_rqtl2_bundle.py | 19 |
1 files changed, 11 insertions, 8 deletions
diff --git a/scripts/process_rqtl2_bundle.py b/scripts/process_rqtl2_bundle.py index 20cfd3b..ade9862 100644 --- a/scripts/process_rqtl2_bundle.py +++ b/scripts/process_rqtl2_bundle.py @@ -2,6 +2,7 @@ import sys import uuid import json +import argparse import traceback from typing import Any from pathlib import Path @@ -94,10 +95,11 @@ def process_bundle(dbconn: mdb.Connection, logger.info("Processing geno files.") genoexit = install_genotypes( dbconn, - meta["speciesid"], - meta["populationid"], - meta["geno-dataset-id"], - Path(meta["rqtl2-bundle-file"]), + argparse.Namespace( + speciesid=meta["speciesid"], + populationid=meta["populationid"], + datasetid=meta["geno-dataset-id"], + rqtl2bundle=Path(meta["rqtl2-bundle-file"])), logger) if genoexit != 0: raise Exception("Processing 'geno' file failed.") @@ -109,10 +111,11 @@ def process_bundle(dbconn: mdb.Connection, if has_pheno_file(thejob): phenoexit = install_pheno_files( dbconn, - meta["speciesid"], - meta["platformid"], - meta["probe-dataset-id"], - Path(meta["rqtl2-bundle-file"]), + argparse.Namespace( + speciesid=meta["speciesid"], + platformid=meta["platformid"], + dataset_id=meta["probe-dataset-id"], + rqtl2bundle=Path(meta["rqtl2-bundle-file"])), logger) if phenoexit != 0: raise Exception("Processing 'pheno' file failed.") |