this cuts the count file produced from featureCounts down to
    a two column file of gene ids and number of reads mapping to
    each gene

def _format_count_file(count_file, data):
    """
    this cuts the count file produced from featureCounts down to
    a two column file of gene ids and number of reads mapping to
    each gene
    """
    COUNT_COLUMN = 5
    out_file = os.path.splitext(count_file)[0] + ".fixed.counts"
    if file_exists(out_file):
        return out_file

    df = pd.io.parsers.read_table(count_file, sep="\t", index_col=0, header=1)
    df_sub = df.ix[:, COUNT_COLUMN]
    with file_transaction(data, out_file) as tx_out_file:
        df_sub.to_csv(tx_out_file, sep="\t", index_label="id", header=False)
    return out_file