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"""Run quality control on phenotypes-specific files in the bundle."""
import sys
from pathlib import Path
from argparse import ArgumentParser
from logging import Logger, getLogger, StreamHandler
import MySQLdb as mdb
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 scripts.rqtl2.entry import build_main
from scripts.rqtl2.cli_parser import add_bundle_argument
def validate(phenobundle: Path, logger: Logger) -> dict:
"""Check that the bundle is generally valid"""
try:
rqc.validate_bundle(phenobundle)
except rqe.RQTLError as rqtlerr:
# logger.error("Bundle file validation failed!", exc_info=True)
return {
"skip": True,
"logger": logger,
"phenobundle": phenobundle,
"errors": (" ".join(rqtlerr.args),)
}
return {
"errors": tuple(),
"skip": False,
"phenobundle": phenobundle,
"logger": logger
}
def check_for_mandatory_pheno_keys(
phenobundle: Path,
logger: Logger,
**kwargs
) -> dict:
"""Check that the mandatory keys exist for phenotypes."""
if kwargs.get("skip", False):
return {
**kwargs,
"logger": logger,
"phenobundle": phenobundle
}
_mandatory_keys = ("pheno", "phenocovar")
_cdata = rqtl2.read_control_file(phenobundle)
_errors = kwargs.get("errors", tuple()) + tuple(
f"Expected '{key}' file(s) are not declared in the bundle."
for key in _mandatory_keys if key not in _cdata.keys())
return {
**kwargs,
"logger": logger,
"phenobundle": phenobundle,
"errors": _errors,
"skip": len(_errors) > 0
}
def check_for_averages_files(
phenobundle: Path,
logger: Logger,
**kwargs
) -> dict:
"""Check that averages files appear together"""
if kwargs.get("skip", False):
return {
**kwargs,
"logger": logger,
"phenobundle": phenobundle
}
_together = (("phenose", "phenonum"), ("phenonum", "phenose"))
_cdata = rqtl2.read_control_file(phenobundle)
_errors = kwargs.get("errors", tuple()) + tuple(
f"'{first}' is defined in the control file but there is no "
f"corresponding '{second}'"
for first, second in _together
if ((first in _cdata.keys()) and (second not in _cdata.keys())))
return {
**kwargs,
"logger": logger,
"phenobundle": phenobundle,
"errors": _errors,
"skip": len(_errors) > 0
}
def run_qc(dbconn: mdb.Connection, phenobundle: Path, logger: Logger) -> int:
"""Run quality control checks on the bundle."""
results = check_for_averages_files(
**check_for_mandatory_pheno_keys(
**validate(phenobundle, logger)))
errors = results.get("errors", tuple())
if len(errors) > 0:
logger.error("We found the following errors:\n%s",
"\n".join(f" - {error}" for error in errors))
return 1
# TODO: Run QC on actual values
# Steps:
# - Extract file to specific directory
# - For every pheno, phenocovar, phenose, phenonum file, undo
# transposition where relevant
# - Check that `description` and `units` is present in phenocovar for
# all phenotypes
# - Check all phenotypes in pheno files exist in phenocovar files
# - Check all numeric values
raise NotImplementedError("WIP!")
if __name__ == "__main__":
def cli_args():
"""Process command-line arguments for `install_phenos`"""
parser = add_bundle_argument(init_cli_parser(
program="PhenotypesQC",
description=(
"Perform Quality Control checks on a phenotypes bundle file")))
return parser.parse_args()
_logger = getLogger("phenotypes_qc")
_logger.addHandler(StreamHandler(stream=sys.stderr))
main = build_main(
cli_args(),
lambda dbconn, args: run_qc(dbconn, args.rqtl2bundle, _logger),
_logger,
"DEBUG")
sys.exit(main())
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