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Merged
joshua-gould merged 2 commits into from
Jun 18, 2026
Merged

merge-cols #161

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07b9d27
Check for unique columns
joshua-gould Jun 18, 2026
ba6bfca
Check for unique columns
joshua-gould Jun 18, 2026
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7 changes: 6 additions & 1 deletion scallops/cli/pooled_if_sbs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -481,6 +481,7 @@ def _rename_unique(columns, unique_values, prefix):
replace_chars = " |-"
for value in columns:
new_value = value
new_value = re.sub(replace_chars, "_", new_value)
if value in unique_values:
new_value = f"{value}_{prefix}"
if new_value in unique_values:
Expand All @@ -489,7 +490,7 @@ def _rename_unique(columns, unique_values, prefix):
while new_value in unique_values:
counter += 1
new_value = f"{value}_{prefix}_{counter}"
new_value = re.sub(replace_chars, "_", new_value)

if value != new_value:
rename[value] = new_value

Expand Down Expand Up @@ -614,6 +615,10 @@ def merge_sbs_phenotype_pipeline(
df_phenotype = pd.concat(df_phenotypes, axis=1, join=join_phenotype)
elif len(df_phenotypes) == 1:
df_phenotype = df_phenotypes[0]
if df_phenotype is not None:
assert not df_phenotype.columns.has_duplicates, (
f"Duplicate columns: {', '.join(df_phenotype.columns[df_phenotype.columns.duplicated()].to_list())}"
)
if df_labels is not None and df_phenotype is not None and df_barcode is not None:
merged_df = merge_sbs_phenotype(
df_labels=df_labels,
Expand Down