def _merge_rna(paths, metadata, save_dir, id_col="lane_id", parallel=True):
""""""
# TODO: significant memory leakage -- maybe make an optional kwarg
if parallel:
pool = Parallel(n_jobs=-2)
rna_list = pool(
delayed(Counts.from_cellranger)(path) for path in paths)
else:
rna_list = [Counts.from_cellranger(path) for path in paths]
widths = list(map(lambda x: x.shape[1], rna_list))
if len(set(widths)) > 1:
raise ValueError(
f"Can't merge matrices with mixed shapes: {set(widths)}. Details: {list(zip(paths, widths))}"
)
rna = Counts.concatenate(rna_list)
meta = None
if metadata is not None:
metadata_cols = [
col for col in metadata.columns if not col.startswith("path_")
]
metadata = metadata[metadata_cols]
cells_per_matrix = [counts.shape[0] for counts in rna_list]
meta = metadata.loc[metadata.index.repeat(
cells_per_matrix)].reset_index(drop=True)
if id_col in metadata:
rna.index = rna.index.str.slice(0,
-1) + meta[id_col].astype(str)
if rna.index.duplicated().any():
raise ValueError(
"cell identifiers must be unique. Consider using metadata with `lane_id` column or specify a custom "
"`id_col")
if meta is None:
meta = pd.DataFrame(index=rna.cell_ids)
meta.index.name = None
else:
meta = pd.DataFrame(meta)
meta.index = rna.cell_ids
if save_dir:
os.makedirs(save_dir, exist_ok=True)
meta.to_csv(save_dir / "meta.tsv", sep="\t")
# TODO: move create_rds val to config
rna.save(save_dir / "rna.pickle", save_rds=True)
return rna, meta
def _merge_rna(paths, metadata, save_dir):
""""""
rna_list = [Counts.from_cellranger(dir_) for dir_ in paths]
meta = None
if metadata is not None:
metadata_cols = [
col for col in metadata.columns if not col.startswith("path_")
]
metadata = metadata[metadata_cols]
cells_per_matrix = [counts.shape[0] for counts in rna_list]
meta = metadata.loc[metadata.index.repeat(
cells_per_matrix)].reset_index(drop=True)
rna = Counts.concatenate(rna_list)
if meta is not None:
meta.index = rna.cell_ids
else:
meta = rna.cell_ids
if save_dir:
os.makedirs(save_dir, exist_ok=True)
meta.to_csv(save_dir / "meta.tsv", sep="\t")
# TODO: move create_rds val to config
rna.save(save_dir / "rna.pickle", create_rds=True)
return rna, meta