proteobench package

ProteoBench.

Subpackages

• proteobench.datapoint package
  • DatapointBase
    • DatapointBase.generate_datapoint()
    • DatapointBase.generate_id()
    • DatapointBase.get_metrics()
  • QuantDatapointHYE
    • QuantDatapointHYE.id
    • QuantDatapointHYE.software_name
    • QuantDatapointHYE.software_version
    • QuantDatapointHYE.search_engine
    • QuantDatapointHYE.search_engine_version
    • QuantDatapointHYE.ident_fdr_psm
    • QuantDatapointHYE.ident_fdr_peptide
    • QuantDatapointHYE.ident_fdr_protein
    • QuantDatapointHYE.enable_match_between_runs
    • QuantDatapointHYE.precursor_mass_tolerance
    • QuantDatapointHYE.fragment_mass_tolerance
    • QuantDatapointHYE.enzyme
    • QuantDatapointHYE.allowed_miscleavages
    • QuantDatapointHYE.min_peptide_length
    • QuantDatapointHYE.max_peptide_length
    • QuantDatapointHYE.is_temporary
    • QuantDatapointHYE.intermediate_hash
    • QuantDatapointHYE.results
    • QuantDatapointHYE.median_abs_epsilon_global
    • QuantDatapointHYE.mean_abs_epsilon_global
    • QuantDatapointHYE.median_abs_epsilon_eq_species
    • QuantDatapointHYE.mean_abs_epsilon_eq_species
    • QuantDatapointHYE.median_abs_epsilon_precision_global
    • QuantDatapointHYE.mean_abs_epsilon_precision_global
    • QuantDatapointHYE.median_abs_epsilon_precision_eq_species
    • QuantDatapointHYE.mean_abs_epsilon_precision_eq_species
    • QuantDatapointHYE.nr_prec
    • QuantDatapointHYE.comments
    • QuantDatapointHYE.proteobench_version
    • QuantDatapointHYE.allowed_miscleavages
    • QuantDatapointHYE.comments
    • QuantDatapointHYE.enable_match_between_runs
    • QuantDatapointHYE.enzyme
    • QuantDatapointHYE.fragment_mass_tolerance
    • QuantDatapointHYE.generate_datapoint()
    • QuantDatapointHYE.generate_id()
    • QuantDatapointHYE.get_cv_metrics()
    • QuantDatapointHYE.get_epsilon_metrics()
    • QuantDatapointHYE.get_metrics()
    • QuantDatapointHYE.get_precision_metrics()
    • QuantDatapointHYE.id
    • QuantDatapointHYE.ident_fdr_peptide
    • QuantDatapointHYE.ident_fdr_protein
    • QuantDatapointHYE.ident_fdr_psm
    • QuantDatapointHYE.intermediate_hash
    • QuantDatapointHYE.is_temporary
    • QuantDatapointHYE.max_peptide_length
    • QuantDatapointHYE.mean_abs_epsilon_eq_species
    • QuantDatapointHYE.mean_abs_epsilon_global
    • QuantDatapointHYE.mean_abs_epsilon_precision_eq_species
    • QuantDatapointHYE.mean_abs_epsilon_precision_global
    • QuantDatapointHYE.median_abs_epsilon_eq_species
    • QuantDatapointHYE.median_abs_epsilon_global
    • QuantDatapointHYE.median_abs_epsilon_precision_eq_species
    • QuantDatapointHYE.median_abs_epsilon_precision_global
    • QuantDatapointHYE.min_peptide_length
    • QuantDatapointHYE.nr_prec
    • QuantDatapointHYE.precursor_mass_tolerance
    • QuantDatapointHYE.proteobench_version
    • QuantDatapointHYE.results
    • QuantDatapointHYE.search_engine
    • QuantDatapointHYE.search_engine_version
    • QuantDatapointHYE.software_name
    • QuantDatapointHYE.software_version
  • Submodules
    • proteobench.datapoint.datapoint_base module
      • DatapointBase
    • proteobench.datapoint.denovo_datapoint module
      • DenovoDatapoint
      • calculate_prc()
      • collapse_aa_scores()
      • get_prc_curve()
    • proteobench.datapoint.quant_datapoint module
      • QuantDatapointHYE
      • QuantDatapointPYE
      • compute_roc_auc()
      • compute_roc_auc_directional()
      • filter_df_numquant_epsilon()
      • filter_df_numquant_nr_prec()
• proteobench.github namespace
  • Submodules
    • proteobench.github.gh module
      • GithubProteobotRepo
      • get_submission_source()
      • is_official_server()
• proteobench.io package
  • Subpackages
    • proteobench.io.params package
      • Classes
      • Functions
      • ProteoBenchParameters
      • normalize_dataframe_columns()
      • Submodules
    • proteobench.io.parsing package
      • Submodules
• proteobench.modules package
  • Subpackages
    • proteobench.modules.denovo package
      • Submodules
    • proteobench.modules.quant package
      • Submodules
    • proteobench.modules.rescoring package
      • Submodules
  • Submodules
    • proteobench.modules.constants module
• proteobench.plotting package
  • LFQHYEPlotGenerator
    • LFQHYEPlotGenerator.generate_in_depth_plots()
    • LFQHYEPlotGenerator.get_in_depth_plot_descriptions()
    • LFQHYEPlotGenerator.get_in_depth_plot_layout()
    • LFQHYEPlotGenerator.plot_main_metric()
  • PlotGeneratorBase
    • PlotGeneratorBase.generate_in_depth_plots()
    • PlotGeneratorBase.get_in_depth_plot_descriptions()
    • PlotGeneratorBase.get_in_depth_plot_layout()
    • PlotGeneratorBase.plot_main_metric()
  • Submodules
    • proteobench.plotting.plot_generator_base module
      • PlotGeneratorBase
    • proteobench.plotting.plot_generator_denovo module
      • DeNovoPlotGenerator
      • flatten_results_column()
    • proteobench.plotting.plot_generator_lfq_HYE module
      • LFQHYEPlotGenerator
    • proteobench.plotting.plot_generator_lfq_PYE module
      • LFQPYEPlotGenerator
• proteobench.score package
  • QuantScoresHYE
    • QuantScoresHYE.compute_condition_stats()
    • QuantScoresHYE.compute_epsilon()
    • QuantScoresHYE.convert_replicate_to_raw()
    • QuantScoresHYE.generate_intermediate()
  • ScoreBase
    • ScoreBase.generate_intermediate()
  • Submodules
    • proteobench.score.denovoscores module
      • DenovoScores
    • proteobench.score.quantscoresHYE module
      • QuantScoresHYE
    • proteobench.score.quantscoresPYE module
      • QuantScoresPYE
    • proteobench.score.score_base module
      • ScoreBase
• proteobench.utils package
  • Submodules
    • proteobench.utils.get_plots module
    • proteobench.utils.server_io module
      • dataset_folder_exists()
      • download_file()
      • get_merged_json()
      • get_raw_data()
      • make_submission()
    • proteobench.utils.submission module
      • get_submission_dict()
• proteobench.validation package
  • Check
    • Check.name
    • Check.func
    • Check.description
    • Check.description
    • Check.func
    • Check.name
    • Check.run()
  • FastaReference
    • FastaReference.contains()
    • FastaReference.contains_any()
    • FastaReference.from_bytes()
    • FastaReference.from_identifiers()
    • FastaReference.from_path()
    • FastaReference.from_text()
    • FastaReference.from_url()
    • FastaReference.identifiers
  • ModuleValidationConfig
    • ModuleValidationConfig.protein_column
    • ModuleValidationConfig.sequence_column
    • ModuleValidationConfig.charge_column
    • ModuleValidationConfig.proforma_column
    • ModuleValidationConfig.contaminant_column
    • ModuleValidationConfig.contaminant_flag
    • ModuleValidationConfig.decoy_prefixes
    • ModuleValidationConfig.protein_group_separators
    • ModuleValidationConfig.fasta_url
    • ModuleValidationConfig.fasta_filename
    • ModuleValidationConfig.species_flags
    • ModuleValidationConfig.recommended_max_fdr_psm
    • ModuleValidationConfig.max_plausible_ppm
    • ModuleValidationConfig.max_plausible_dalton
    • ModuleValidationConfig.validation_profile
    • ModuleValidationConfig.charge_column
    • ModuleValidationConfig.contaminant_column
    • ModuleValidationConfig.contaminant_flag
    • ModuleValidationConfig.decoy_prefixes
    • ModuleValidationConfig.fasta_filename
    • ModuleValidationConfig.fasta_url
    • ModuleValidationConfig.from_parse_settings()
    • ModuleValidationConfig.max_plausible_dalton
    • ModuleValidationConfig.max_plausible_ppm
    • ModuleValidationConfig.proforma_column
    • ModuleValidationConfig.protein_column
    • ModuleValidationConfig.protein_group_separators
    • ModuleValidationConfig.read_reference_database()
    • ModuleValidationConfig.recommended_max_fdr_psm
    • ModuleValidationConfig.sequence_column
    • ModuleValidationConfig.species_flags
    • ModuleValidationConfig.validation_profile
  • Severity
    • Severity.ERROR
    • Severity.INFO
    • Severity.WARNING
  • SubmissionValidationError
  • ValidationContext
    • ValidationContext.standard_df
    • ValidationContext.parameters
    • ValidationContext.config
    • ValidationContext.fasta
    • ValidationContext.input_format
    • ValidationContext.reference
    • ValidationContext.extras
    • ValidationContext.config
    • ValidationContext.extras
    • ValidationContext.fasta
    • ValidationContext.input_format
    • ValidationContext.parameters
    • ValidationContext.reference
    • ValidationContext.standard_df
  • ValidationIssue
    • ValidationIssue.code
    • ValidationIssue.severity
    • ValidationIssue.message
    • ValidationIssue.check
    • ValidationIssue.field
    • ValidationIssue.observed
    • ValidationIssue.expected
    • ValidationIssue.examples
    • ValidationIssue.check
    • ValidationIssue.code
    • ValidationIssue.examples
    • ValidationIssue.expected
    • ValidationIssue.field
    • ValidationIssue.message
    • ValidationIssue.observed
    • ValidationIssue.severity
    • ValidationIssue.to_dict()
  • ValidationProfile
    • ValidationProfile.name
    • ValidationProfile.checks
    • ValidationProfile.description
    • ValidationProfile.check_names
    • ValidationProfile.checks
    • ValidationProfile.description
    • ValidationProfile.name
  • ValidationReport
    • ValidationReport.issues
    • ValidationReport.add()
    • ValidationReport.add_error()
    • ValidationReport.add_info()
    • ValidationReport.add_warning()
    • ValidationReport.errors
    • ValidationReport.extend()
    • ValidationReport.has_errors
    • ValidationReport.infos
    • ValidationReport.issues
    • ValidationReport.passed
    • ValidationReport.raise_if_errors()
    • ValidationReport.summary()
    • ValidationReport.to_dict()
    • ValidationReport.warnings
  • available_profiles()
  • get_profile()
  • register_profile()
  • unregister_profile()
  • validate_submission()
  • Submodules
    • proteobench.validation.checks module
      • MAX_PROTEIN_EXAMPLES
      • MAX_ROW_EXAMPLES
      • check_charge_range()
      • check_enzyme()
      • check_fdr_psm()
      • check_mass_tolerances()
      • check_max_modifications()
      • check_modifications()
      • check_peptide_length()
      • check_protein_ids()
      • check_run_consistency()
    • proteobench.validation.config module
      • DEFAULT_DECOY_PREFIXES
      • DEFAULT_VALIDATION_PROFILE
      • ModuleValidationConfig
    • proteobench.validation.context module
      • ValidationContext
    • proteobench.validation.exceptions module
      • Classes
      • SubmissionValidationError
    • proteobench.validation.fasta module
      • FastaReference
      • parse_fasta_header()
    • proteobench.validation.profiles module
      • Check
      • CheckFunc
      • ValidationProfile
      • available_profiles()
      • get_profile()
      • register_profile()
      • unregister_profile()
    • proteobench.validation.protein_ids module
      • DEFAULT_GROUP_SEPARATORS
      • extract_identifiers()
      • is_decoy_or_contaminant()
      • split_protein_groups()
    • proteobench.validation.report module
      • Severity
      • ValidationIssue
      • ValidationReport
    • proteobench.validation.validator module
      • validate_submission()

Submodules

• proteobench.exceptions module
  • ConvertStandardFormatError
  • DatapointAppendError
  • DatapointGenerationError
  • DatasetAlreadyExistsOnServerError
  • IntermediateFormatGenerationError
  • ParseError
  • ParseSettingsError
  • PlotError
  • ProteoBenchError
  • ProteobenchError
  • QuantificationError
  • ValidationError