proteobench.io.parsing package

Package for parsing data from various sources.

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
    • ParseModificationSettings.convert_to_proforma()
  • ParseSettingsBuilder
    • ParseSettingsBuilder.build_parser()
  • ParseSettingsDeNovo
    • ParseSettingsDeNovo.add_features()
    • ParseSettingsDeNovo.add_modification_parser()
    • ParseSettingsDeNovo.convert_to_standard_format()
    • ParseSettingsDeNovo.extract_scan_id()
    • ParseSettingsDeNovo.format_scores()
    • ParseSettingsDeNovo.format_sequence()
    • ParseSettingsDeNovo.get_length_peptidoform_with_nterm()
  • ParseSettingsQuant
    • ParseSettingsQuant.add_modification_parser()
    • ParseSettingsQuant.convert_to_standard_format()
    • ParseSettingsQuant.species_dict()
    • ParseSettingsQuant.species_expected_ratio()
  • get_open_source_tools()
• proteobench.io.parsing.utils module
  • add_fixed_mod()
  • add_maxquant_fixed_modifications()