proteobench.io.params package

This module provides the ProteoBenchParameters dataclass for handling parameters related to ProteoBench. The parsing is done per data analysis software.

Classes ProteoBenchParameters

A dataclass for handling ProteoBench parameters.

class proteobench.io.params.ProteoBenchParameters(filename='/home/docs/checkouts/readthedocs.org/user_builds/proteobench/envs/v0.10.4/lib/python3.11/site-packages/proteobench/io/params/json/Quant/quant_lfq_DDA_ion.json', **kwargs)

Bases: object

ProteoBench parameter dataclass.

Parameters:

• filename (os.path) – Path to parameter file.

• **kwargs (dict[str, Any]) – Other keyword arguments.

fill_none()

Fill all None values with np.nan.

Submodules

• 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.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
    • Parameter.comment
    • Parameter.name
    • Parameter.value
  • extract_params()
  • parse_params()
  • parse_phi_report_filters()
  • read_fragpipe_workflow()
• proteobench.io.params.i2masschroq 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.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()