def parse_file(file_name):
    """
    Parses file generated by the filtering script

    :param file_name:
    :return: nested list of all counts, nested list of gene IDs/symbols, list of sample names
    """
    all_counts = []
    gene_names = []
    with open(file_name, "r") as file:
        header = next(file)
        header_splitted = header.split("\n")[0].split("\t")
        ids_file = header_splitted[2:]
        for line in file:
            splitted = line.split("\n")[0].split("\t")
            count_line = splitted[2:]
            gene_name = splitted[:2]
            gene_names.append(gene_name)
            all_counts.append(count_line)
    return all_counts, gene_names, ids_file