def check_for_features(cmph5_file, feature_list):
    """Check that all required features present in the cmph5_file. Return
    a list of features that are missing.
    """

    aln_group_path = cmph5_file['AlnGroup/Path'][0]
    missing_features = []
    for feature in feature_list:
        if feature not in cmph5_file[aln_group_path].keys():
            missing_features.append(feature)

    return missing_features