Merge pull request #277 from NCI-CGR/correct_test_scripts

Correct column name for analytic_exclusion

src/cgr_gwas_qc/workflow/scripts/sample_qc_table.py

@@ -192,7 +192,9 @@ def main(
     )
 
     add_qc_columns(
-        sample_qc, remove_contam, remove_rep_discordant,
+        sample_qc,
+        remove_contam,
+        remove_rep_discordant,
     )
     sample_qc["is_unexpected_replicate"] = (
         sample_qc["is_unexpected_replicate"].replace("", False).fillna(False)
@@ -413,7 +415,8 @@ def _read_contam(file_name: Optional[Path], Sample_IDs: pd.Index) -> pd.DataFram
 
     if file_name is None:
         return pd.DataFrame(
-            index=Sample_IDs, columns=["Contamination_Rate", "is_contaminated"],
+            index=Sample_IDs,
+            columns=["Contamination_Rate", "is_contaminated"],
         ).astype({"Contamination_Rate": "float", "is_contaminated": "boolean"})
 
     return (
@@ -456,12 +459,16 @@ def _read_intensity(file_name: Optional[Path], Sample_IDs: pd.Index) -> pd.Serie
 
 
 def add_qc_columns(
-    sample_qc: pd.DataFrame, remove_contam: bool, remove_rep_discordant: bool,
+    sample_qc: pd.DataFrame,
+    remove_contam: bool,
+    remove_rep_discordant: bool,
 ) -> pd.DataFrame:
     add_call_rate_flags(sample_qc)
     _add_identifiler(sample_qc)
     _add_analytic_exclusion(
-        sample_qc, remove_contam, remove_rep_discordant,
+        sample_qc,
+        remove_contam,
+        remove_rep_discordant,
     )
     _add_subject_representative(sample_qc)
     _add_subject_dropped_from_study(sample_qc)
@@ -507,7 +514,9 @@ def reason_string(row: pd.Series) -> str:
 
 
 def _add_analytic_exclusion(
-    sample_qc: pd.DataFrame, remove_contam: bool, remove_rep_discordant: bool,
+    sample_qc: pd.DataFrame,
+    remove_contam: bool,
+    remove_rep_discordant: bool,
 ) -> pd.DataFrame:
     """Adds a flag to remove samples based on provided conditions.
 
@@ -527,7 +536,7 @@ def _add_analytic_exclusion(
         exclusion_criteria["is_contaminated"] = "Contamination"
 
     if remove_rep_discordant:
-        exclusion_criteria["is_discordant_replicate"] = "Replicate Discordance"
+        exclusion_criteria["Expected Replicate Discordance"] = "Replicate Discordance"
 
     sample_qc["analytic_exclusion"] = sample_qc.reindex(exclusion_criteria.keys(), axis=1).any(
         axis=1