From 6db0d80b595ccd18d18e941f6cda729f4cb393ce Mon Sep 17 00:00:00 2001 From: Mamie Wang Date: Mon, 15 Jul 2024 10:31:56 -0400 Subject: [PATCH] Corrected a bug in finding metadata column names --- bin/postprocessing.py | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/bin/postprocessing.py b/bin/postprocessing.py index af932e6..3015991 100644 --- a/bin/postprocessing.py +++ b/bin/postprocessing.py @@ -73,16 +73,18 @@ def RunPCA(cts, var_threshold, n_components): action=argparse.BooleanOptionalAction, help="Use SCVI latent variable instead of PCA.", ) -parser.add_argument("--metadata", required=False, default="", help="Metadata to be added to obs.") +parser.add_argument( + "--metadata", required=False, default="", help="Metadata to be added to obs." +) args = parser.parse_args() adata = sc.read_h5ad(args.input_h5ad) if not args.metadata == "": metadata = pd.read_csv(args.metadata) - new_cols = [x for x in metadata.cols if x not in adata.obs.columns] - intersect_cols = [x for x in metadata.cols if x in adata.obs.columns] - metadata = adata.obs.merge(metadata, how = 'left', on = intersect_cols) + new_cols = [x for x in metadata.columns if x not in adata.obs.columns] + intersect_cols = [x for x in metadata.columns if x in adata.obs.columns] + metadata = adata.obs.merge(metadata, how="left", on=intersect_cols) assert metadata.shape[0] == adata.shape[0] for new_col in new_cols: adata.obs[new_col] = metadata[new_col]