code: def run_dependent_peptides(allPeptides_file, rawFilesTable_file, outfile):
      
      __dep, localization = read_dependent_peptides(allPeptides_file)
      exp = read_rawFilesTable(rawFilesTable_file)
      _dep = _set_column_names(__dep, exp)
      main_columns = list(_dep.columns)
      dep = _dep.join(localization).reset_index()
      dep.to_perseus(outfile, main_columns=main_columns)
docs: transform a allPeptides.txt and experimentalDesign.txt table
      into the dependentPeptides.txt table written in outfile.
      :param allPeptides_file: MaxQuant 'allPeptides.txt' output table.
      :param rawFilesTable_file: MaxQuant 'Raw files'-tab table.
      :param outfile: Path to the output file.