diff options
Diffstat (limited to 'scripts/rqtl2')
| -rw-r--r-- | scripts/rqtl2/phenotypes_qc.py | 16 |
1 files changed, 8 insertions, 8 deletions
diff --git a/scripts/rqtl2/phenotypes_qc.py b/scripts/rqtl2/phenotypes_qc.py index a9097d5..699c291 100644 --- a/scripts/rqtl2/phenotypes_qc.py +++ b/scripts/rqtl2/phenotypes_qc.py @@ -181,7 +181,7 @@ def qc_phenocovar_file( filepath.name, f"{fqkey}:logs") as logger, Redis.from_url(redisuri, decode_responses=True) as rconn): - logger.info("Running QC on file: %s", filepath.name) + print("Running QC on file: ", filepath.name) _csvfile = rqtl2.read_csv_file(filepath, separator, comment_char) _headings = tuple(heading.lower() for heading in next(_csvfile)) _errors: tuple[InvalidValue, ...] = tuple() @@ -289,7 +289,7 @@ def qc_pheno_file(# pylint: disable=[too-many-locals, too-many-arguments] filepath.name, f"{fqkey}:logs") as logger, Redis.from_url(redisuri, decode_responses=True) as rconn): - logger.info("Running QC on file: %s", filepath.name) + print("Running QC on file: ", filepath.name) save_error = partial( push_error, rconn, file_fqkey(fqkey, "errors", filepath)) _csvfile = rqtl2.read_csv_file(filepath, separator, comment_char) @@ -376,7 +376,7 @@ def run_qc(# pylint: disable=[too-many-locals] args: Namespace ) -> int: """Run quality control checks on the bundle.""" - logger.debug("Beginning the quality assurance checks.") + print("Beginning the quality assurance checks.") results = check_for_averages_files( **check_for_mandatory_pheno_keys( **validate(args.rqtl2bundle, logger))) @@ -401,7 +401,7 @@ def run_qc(# pylint: disable=[too-many-locals] for ftype in ("pheno", "phenocovar", "phenose", "phenonum"))) # - Fetch samples/individuals from database. - logger.debug("Fetching samples/individuals from the database.") + print("Fetching samples/individuals from the database.") samples = tuple(#type: ignore[var-annotated] item for item in set(reduce( lambda acc, item: acc + ( @@ -418,7 +418,7 @@ def run_qc(# pylint: disable=[too-many-locals] json.dumps(tuple(f"{fullyqualifiedjobid}:phenocovar:{_file}" for _file in cdata.get("phenocovar", [])))) with mproc.Pool(mproc.cpu_count() - 1) as pool: - logger.debug("Check for errors in 'phenocovar' file(s).") + print("Check for errors in 'phenocovar' file(s).") _phenocovar_qc_res = merge_dicts(*pool.starmap(qc_phenocovar_file, tuple( (extractiondir.joinpath(_file), args.redisuri, @@ -440,7 +440,7 @@ def run_qc(# pylint: disable=[too-many-locals] "Expected a non-negative number with at least one decimal " "place.")) - logger.debug("Check for errors in 'pheno' file(s).") + print("Check for errors in 'pheno' file(s).") _pheno_qc_res = merge_dicts(*pool.starmap(qc_pheno_file, tuple(( extractiondir.joinpath(_file), args.redisuri, @@ -459,7 +459,7 @@ def run_qc(# pylint: disable=[too-many-locals] # - Check the 3 checks above for phenose and phenonum values too # qc_phenose_files(…) # qc_phenonum_files(…) - logger.debug("Check for errors in 'phenose' file(s).") + print("Check for errors in 'phenose' file(s).") _phenose_qc_res = merge_dicts(*pool.starmap(qc_pheno_file, tuple(( extractiondir.joinpath(_file), args.redisuri, @@ -475,7 +475,7 @@ def run_qc(# pylint: disable=[too-many-locals] dec_err_fn ) for _file in cdata.get("phenose", [])))) - logger.debug("Check for errors in 'phenonum' file(s).") + print("Check for errors in 'phenonum' file(s).") _phenonum_qc_res = merge_dicts(*pool.starmap(qc_pheno_file, tuple(( extractiondir.joinpath(_file), args.redisuri, |