fix for count column not found

hubmapconsortium · Nov 28, 2023 · 4fb1983 · 4fb1983
1 parent 6212441
commit 4fb1983
Showing 1 changed file with 1 addition and 0 deletions.
diff --git a/containers/extract-summary/context/main.py b/containers/extract-summary/context/main.py
@@ -9,6 +9,7 @@ def get_unique_rows_with_counts(
  matrix: anndata.AnnData, clid_column: str
 ) -> pd.DataFrame:
  counts = matrix.obs.value_counts(clid_column).reset_index()
+ counts.columns = [clid_column, "count"]
  obs_with_counts = matrix.obs.merge(counts, how="left")
  return obs_with_counts.drop_duplicates(clid_column)