read the dependent peptides table and extract localiztion information
    :param filename: path to the 'allPeptides.txt' table.
    :returns dep, localization: the dependent peptide table, localization information.

def read_dependent_peptides(filename):
    """ read the dependent peptides table and extract localiztion information
    :param filename: path to the 'allPeptides.txt' table.
    :returns dep, localization: the dependent peptide table, localization information.
    """
    df = (pd.read_perseus(filename, usecols=_cols)
            .dropna(subset=['DP Ratio mod/base']))
    df['DP Ratio mod/base'] = df['DP Ratio mod/base'].astype(float)
    dep = df.pivot_table('DP Ratio mod/base', index=_index_columns,
                columns='Raw file', aggfunc=np.median)
    localization = _count_localizations(df)
    return dep, localization