import loompy import pandas as pd def loom_to_pandas_df(file_name="testfiles/test.loom"): """ :param file_name: the name of the loom file (default is: "testfiles/test.loom") :return: pandas DataFrame """ df = pd.DataFrame # Empty DataFrame - to return in case of wrong formatting if file_name[-4:] != ".loom": print(f"{file_name} is not a valid file name. Only use '.loom' files!") with loompy.connect(file_name) as ds: try: df = pd.DataFrame(data=ds[:, :], index=ds.ra.Gene, columns=ds.ca.input_name) except AttributeError or ValueError or OSError: raise Exception(f"The loom file {file_name} does not exist or has no valid format!") return df