diff --git a/MIMIC-IV_Example/pre_MEDS.py b/MIMIC-IV_Example/pre_MEDS.py index 846c3a9..d8b39ba 100755 --- a/MIMIC-IV_Example/pre_MEDS.py +++ b/MIMIC-IV_Example/pre_MEDS.py @@ -229,7 +229,7 @@ def main(cfg: DictConfig): ) exit(0) - all_fps = list(input_dir.glob("**/*.*")) + all_fps = list(input_dir.rglob("*/*.*")) dfs_to_load = {} seen_fps = {} @@ -299,9 +299,9 @@ def main(cfg: DictConfig): logger.info(f"Loading {str(df_to_load_fp.resolve())} for manipulating other dataframes...") if df_to_load_fp.suffix in [".csv.gz"]: - df = read_fn(df_to_load_fp, columns=cols) + df = df_to_load_read_fn(df_to_load_fp, columns=cols) else: - df = read_fn(df_to_load_fp) + df = df_to_load_read_fn(df_to_load_fp) logger.info(f" Loaded in {datetime.now() - st}") for fp in fps: