diff options
| -rw-r--r-- | scripts/rqtl2/phenotypes_qc.py | 23 |
1 files changed, 13 insertions, 10 deletions
diff --git a/scripts/rqtl2/phenotypes_qc.py b/scripts/rqtl2/phenotypes_qc.py index 98b855f..9f11f57 100644 --- a/scripts/rqtl2/phenotypes_qc.py +++ b/scripts/rqtl2/phenotypes_qc.py @@ -41,15 +41,18 @@ logging.basicConfig( "(%(pathname)s: %(lineno)d) %(message)s")) logger = logging.getLogger(__MODULE__) -def validate(phenobundle: Path, alogger: Logger) -> dict: +def validate( + phenobundle: Path, + logger: Logger# pylint: disable=[redefined-outer-name] +) -> dict: """Check that the bundle is generally valid""" try: rqc.validate_bundle(phenobundle) except rqe.RQTLError as rqtlerr: - # alogger.error("Bundle file validation failed!", exc_info=True) + # logger.error("Bundle file validation failed!", exc_info=True) return { "skip": True, - "logger": alogger, + "logger": logger, "phenobundle": phenobundle, "errors": (" ".join(rqtlerr.args),) } @@ -57,20 +60,20 @@ def validate(phenobundle: Path, alogger: Logger) -> dict: "errors": tuple(), "skip": False, "phenobundle": phenobundle, - "logger": alogger + "logger": logger } def check_for_mandatory_pheno_keys( phenobundle: Path, - alogger: Logger, + logger: Logger,# pylint: disable=[redefined-outer-name] **kwargs ) -> dict: """Check that the mandatory keys exist for phenotypes.""" if kwargs.get("skip", False): return { **kwargs, - "logger": alogger, + "logger": logger, "phenobundle": phenobundle } @@ -81,7 +84,7 @@ def check_for_mandatory_pheno_keys( for key in _mandatory_keys if key not in _cdata.keys()) return { **kwargs, - "logger": alogger, + "logger": logger, "phenobundle": phenobundle, "errors": _errors, "skip": len(_errors) > 0 @@ -90,14 +93,14 @@ def check_for_mandatory_pheno_keys( def check_for_averages_files( phenobundle: Path, - alogger: Logger, + logger: Logger,# pylint: disable=[redefined-outer-name] **kwargs ) -> dict: """Check that averages files appear together""" if kwargs.get("skip", False): return { **kwargs, - "logger": alogger, + "logger": logger, "phenobundle": phenobundle } @@ -110,7 +113,7 @@ def check_for_averages_files( if ((first in _cdata.keys()) and (second not in _cdata.keys()))) return { **kwargs, - "logger": alogger, + "logger": logger, "phenobundle": phenobundle, "errors": _errors, "skip": len(_errors) > 0 |