diff options
Diffstat (limited to 'scripts/qc_on_rqtl2_bundle.py')
| -rw-r--r-- | scripts/qc_on_rqtl2_bundle.py | 59 |
1 files changed, 42 insertions, 17 deletions
diff --git a/scripts/qc_on_rqtl2_bundle.py b/scripts/qc_on_rqtl2_bundle.py index aea1baa..c3e8b66 100644 --- a/scripts/qc_on_rqtl2_bundle.py +++ b/scripts/qc_on_rqtl2_bundle.py @@ -14,6 +14,7 @@ from qc_app import jobs from qc_app.db_utils import database_connection from qc_app.check_connections import check_db, check_redis +from r_qtl import r_qtl2 as rqtl2 from r_qtl import r_qtl2_qc as rqc from r_qtl import fileerrors as rqfe @@ -59,31 +60,54 @@ def qc_missing_files(rconn: Redis, def qc_geno_errors(rconn, fqjobid, zfile, logger) -> bool: """Check for errors in `geno` file(s).""" logger.info("Checking for errors in the 'geno' file…") - gerrs = tuple(rqc.geno_errors(zfile)) - add_to_errors(rconn, fqjobid, "errors-generic", tuple( - err for err in gerrs if isinstance(err, rqfe.MissingFile))) - add_to_errors(rconn, fqjobid, "errors-geno", tuple( - err for err in gerrs if not isinstance(err, rqfe.MissingFile))) - if len(gerrs) > 0: - logger.error("The 'geno' file has errors.") - return True + cdata = rqtl2.control_data(zfile) + if "geno" in cdata: + gerrs = tuple(rqc.geno_errors(zfile)) + add_to_errors(rconn, fqjobid, "errors-generic", tuple( + err for err in gerrs if isinstance(err, rqfe.MissingFile))) + add_to_errors(rconn, fqjobid, "errors-geno", tuple( + err for err in gerrs if not isinstance(err, rqfe.MissingFile))) + if len(gerrs) > 0: + logger.error("The 'geno' file has errors.") + return True + logger.info("No errors found in the 'geno' file.") return False def qc_pheno_errors(rconn, fqjobid, zfile, logger) -> bool: """Check for errors in `pheno` file(s).""" - logger.info("Checking for errors in the 'pheno' file …") - perrs = tuple(rqc.pheno_errors(zfile)) - add_to_errors(rconn, fqjobid, "errors-generic", tuple( - err for err in perrs if isinstance(err, rqfe.MissingFile))) - add_to_errors(rconn, fqjobid, "errors-pheno", tuple( - err for err in perrs if not isinstance(err, rqfe.MissingFile))) - if len(perrs) > 0: - logger.error("The 'pheno' file has errors.") - return True + logger.info("Checking for errors in the 'pheno' file…") + cdata = rqtl2.control_data(zfile) + if "pheno" in cdata: + perrs = tuple(rqc.pheno_errors(zfile)) + add_to_errors(rconn, fqjobid, "errors-generic", tuple( + err for err in perrs if isinstance(err, rqfe.MissingFile))) + add_to_errors(rconn, fqjobid, "errors-pheno", tuple( + err for err in perrs if not isinstance(err, rqfe.MissingFile))) + if len(perrs) > 0: + logger.error("The 'pheno' file has errors.") + return True + logger.info("No errors found in the 'pheno' file.") return False +def qc_phenose_errors(rconn, fqjobid, zfile, logger) -> bool: + """Check for errors in `phenose` file(s).""" + logger.info("Checking for errors in the 'phenose' file…") + cdata = rqtl2.control_data(zfile) + if "phenose" in cdata: + perrs = tuple(rqc.phenose_errors(zfile)) + add_to_errors(rconn, fqjobid, "errors-generic", tuple( + err for err in perrs if isinstance(err, rqfe.MissingFile))) + add_to_errors(rconn, fqjobid, "errors-phenose", tuple( + err for err in perrs if not isinstance(err, rqfe.MissingFile))) + if len(perrs) > 0: + logger.error("The 'phenose' file has errors.") + return True + + logger.info("No errors found in the 'phenose' file.") + return False + def qc_phenocovar_errors(_rconn, _fqjobid, _zfile, _logger) -> bool: """Check for errors in `phenocovar` file(s).""" return False @@ -104,6 +128,7 @@ def run_qc(rconn: Redis, 1 if any(( qc_geno_errors(rconn, fqjobid, zfile, logger), qc_pheno_errors(rconn, fqjobid, zfile, logger), + qc_phenose_errors(rconn, fqjobid, zfile, logger), qc_phenocovar_errors(rconn, fqjobid, zfile, logger))) else 0) |