proteobench.io package

IO package.

Subpackages

• proteobench.io.params package
  • ProteoBenchParameters
    • ProteoBenchParameters.fill_none()
  • Submodules
    • proteobench.io.params.adanovo module
      • extract_params()
    • proteobench.io.params.alphadia module
      • clean_line()
      • clean_up_parameters()
      • detect_newer_version()
      • extract_params()
      • extract_values_from_nested_lines()
      • initialize_default_parameters()
      • map_keys_to_desired_format()
      • parse_key_value()
      • process_fragment_mz()
      • process_key_value_line()
      • process_precursor_charge()
      • process_precursor_len()
      • process_precursor_mz()
      • read_file_lines()
    • proteobench.io.params.alphapept module
      • extract_params()
    • proteobench.io.params.casanovo module
      • extract_params()
    • proteobench.io.params.deepnovo module
      • extract_params()
    • proteobench.io.params.diann module
      • extract_cfg_parameter()
      • extract_modifications()
      • extract_params()
      • extract_with_regex()
      • find_cmdline_string()
      • parse_cmdline_string()
      • parse_predictors_library()
      • parse_protein_inference_method()
      • parse_quantification_strategy()
      • parse_setting()
    • proteobench.io.params.fragger module
      • Parameter
      • extract_params()
      • parse_params()
      • parse_phi_report_filters()
      • read_fragpipe_workflow()
    • proteobench.io.params.i2masschroq module
      • extract_params()
    • proteobench.io.params.instanovo module
      • extract_params()
    • proteobench.io.params.maxdia module
    • proteobench.io.params.maxquant module
      • add_record()
      • build_Series_from_records()
      • extend_tuple()
      • extend_tuples_with_none()
      • extract_params()
      • flatten_dict_of_dicts()
      • read_file()
      • read_xml_record()
    • proteobench.io.params.metamorpheus module
      • extract_params()
      • format_tolerances()
      • load_files()
      • parse_modifications()
    • proteobench.io.params.msaid module
      • extract_params()
    • proteobench.io.params.msangel module
      • extract_params()
      • extract_params_mascot_specific()
      • extract_params_xtandem_specific()
      • extract_search_engine()
    • proteobench.io.params.peaks module
      • clean_text()
      • extract_mass_tolerance()
      • extract_params()
      • extract_value()
      • extract_value_regex()
      • get_items_between()
    • proteobench.io.params.pihelixnovo module
      • extract_params()
    • proteobench.io.params.piprimenovo module
      • extract_params()
    • proteobench.io.params.pointnovo module
      • extract_params()
    • proteobench.io.params.proline module
      • extract_params()
      • find_charge()
      • find_min_pep_length()
    • proteobench.io.params.quantms module
      • extract_params()
      • load_files()
      • load_parsed_sdrf()
      • load_versions()
    • proteobench.io.params.sage module
      • extract_params()
    • proteobench.io.params.spectronaut module
      • clean_text()
      • extract_calibration_method()
      • extract_mass_tolerance()
      • extract_tolerances()
      • extract_tolerances_with_regex()
      • extract_value()
      • extract_value_regex()
      • read_spectronaut_settings()
    • proteobench.io.params.wombat module
      • extract_params()
• proteobench.io.parsing package
  • Submodules
    • proteobench.io.parsing.parse_denovo module
      • load_input_file()
    • proteobench.io.parsing.parse_ion module
      • aggregate_modification_column()
      • aggregate_modification_sites_column()
      • count_chars()
      • get_proforma_bracketed()
      • get_stripped_seq()
      • load_input_file()
      • match_brackets()
      • to_lowercase()
    • proteobench.io.parsing.parse_peptidoform module
      • aggregate_modification_column()
      • count_chars()
      • get_proforma_bracketed()
      • get_stripped_seq()
      • load_input_file()
      • match_brackets()
      • to_lowercase()
    • proteobench.io.parsing.parse_settings module
      • ParseModificationSettings
      • ParseSettingsBuilder
      • ParseSettingsDeNovo
      • ParseSettingsQuant
    • proteobench.io.parsing.utils module
      • add_fixed_mod()
      • add_maxquant_fixed_modifications()