Reduce number of local variables created in function.

Use the values in the argparse.Namespace object directly to avoid
creating many local variables.

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))