diff options
Diffstat (limited to 'scripts')
| -rw-r--r-- | scripts/cli/options.py | 2 | ||||
| -rw-r--r-- | scripts/run_qtlreaper.py | 15 |
2 files changed, 8 insertions, 9 deletions
diff --git a/scripts/cli/options.py b/scripts/cli/options.py index 67f35dc..70d2a27 100644 --- a/scripts/cli/options.py +++ b/scripts/cli/options.py @@ -13,7 +13,7 @@ def add_logging(parser: ArgumentParser) -> ArgumentParser: type=str, default="INFO", choices=loglevels, - help=(f"Controls the severity of events to log. Valid values are: " + + help=("Controls the severity of events to log. Valid values are: " + ", ".join(f"'{level}'" for level in loglevels))) return parser diff --git a/scripts/run_qtlreaper.py b/scripts/run_qtlreaper.py index ab58203..89cc3ec 100644 --- a/scripts/run_qtlreaper.py +++ b/scripts/run_qtlreaper.py @@ -4,7 +4,6 @@ import csv import time import secrets import logging -import traceback import subprocess from pathlib import Path from typing import Union @@ -86,8 +85,7 @@ def parse_tsv_file(results_file: Path) -> list[dict]: _dialect = csv.unix_dialect() _dialect.delimiter = "\t" reader = csv.DictReader(readptr, dialect=_dialect) - for row in reader: - yield row + yield from reader def __qtls_by_trait__(qtls, current): @@ -99,6 +97,7 @@ def __qtls_by_trait__(qtls, current): def save_qtl_values_to_db(conn, qtls: dict): + """Save computed QTLs to the database.""" with conn.cursor() as cursor: cursor.executemany( "UPDATE PublishXRef SET " @@ -167,16 +166,16 @@ def dispatch(args: Namespace) -> int: _traitsfile.unlink() _qtlreaper_main_output.unlink() logger.info("Successfully computed p values for %s traits.", len(_traitsdata)) - exitcode = 0 + return 0 except FileNotFoundError as fnf: logger.error(", ".join(fnf.args), exc_info=False) except AssertionError as aserr: logger.error(", ".join(aserr.args), exc_info=False) - except Exception as _exc: + except Exception as _exc:# pylint: disable=[broad-exception-caught] logger.debug("Type of exception: %s", type(_exc)) logger.error("General exception!", exc_info=True) - finally: - return exitcode + + return exitcode if __name__ == "__main__": @@ -205,7 +204,7 @@ if __name__ == "__main__": "in the population.")) args = parser.parse_args() setup_logging(logger, args.log_level) - + return dispatch(args) sys.exit(main()) |