diff options
| -rw-r--r-- | scripts/rqtl2/phenotypes_qc.py | 10 |
1 files changed, 5 insertions, 5 deletions
diff --git a/scripts/rqtl2/phenotypes_qc.py b/scripts/rqtl2/phenotypes_qc.py index 2e7937f..83828e4 100644 --- a/scripts/rqtl2/phenotypes_qc.py +++ b/scripts/rqtl2/phenotypes_qc.py @@ -329,12 +329,10 @@ def run_qc(# pylint: disable=[too-many-locals] logger: Logger ) -> int: """Run quality control checks on the bundle.""" - (phenobundle, workingdir, speciesid, populationid) = ( - args.rqtl2bundle, args.workingdir, args.speciesid, args.populationid) logger.debug("Beginning the quality assuarance checks.") results = check_for_averages_files( **check_for_mandatory_pheno_keys( - **validate(phenobundle, logger))) + **validate(args.rqtl2bundle, logger))) errors = results.get("errors", tuple()) if len(errors) > 0: logger.error("We found the following errors:\n%s", @@ -343,7 +341,8 @@ def run_qc(# pylint: disable=[too-many-locals] # Run QC on actual values # Steps: # - Extract file to specific directory - extractiondir, *_bundlefiles = extract_bundle(phenobundle, workingdir) + extractiondir, *_bundlefiles = extract_bundle( + args.rqtl2bundle, args.workingdir, args.jobid) # - For every pheno, phenocovar, phenose, phenonum file, undo # transposition where relevant @@ -360,7 +359,8 @@ def run_qc(# pylint: disable=[too-many-locals] item for item in set(reduce( lambda acc, item: acc + ( item["Name"], item["Name2"], item["Symbol"], item["Alias"]), - samples_by_species_and_population(dbconn, speciesid, populationid), + samples_by_species_and_population( + dbconn, args.speciesid, args.populationid), tuple())) if bool(item)) |