Configuration Data Classes

For scoring, IPF and levels context inference, PyProphet uses configuration data classes to manage settings and parameters. These classes are designed to be easily extensible and provide a structured way to handle configuration options.

Abstract Base Classes

BaseIOConfig

Base configuration class for I/O-related metadata and common attributes used across algorithms.

Scoring Configuration

This module defines configuration classes for various aspects of the scoring, error estimation, and inference processes in PyProphet.

The configurations are implemented using Python’s dataclass to provide a structured and type-safe way to manage parameters. These configurations are used to control the behavior of different components, such as scoring, classifier setup, error estimation, and I/O operations.

Classes:

  • ErrorEstimationConfig: Configuration for global and local FDR (false discovery rate) estimation.

  • RunnerConfig: Configuration for scoring, classifier setup, learning parameters, and optional features.

  • RunnerIOConfig: Wrapper configuration class for I/O and runner parameters.

  • IPFIOConfig: Configuration for Inference of Peptidoforms (IPF).

  • LevelContextIOConfig: Configuration for level-based context inference (e.g., peptide, protein, gene).

- These classes include attributes for controlling various aspects of the pipeline,

such as classifier type, hyperparameter tuning, error estimation methods, and input/output file handling.

Usage:

These configuration classes are typically instantiated with default values or populated from command-line arguments using the from_cli_args class methods.

RunnerIOConfig

Wrapper configuration class for I/O and runner parameters.

RunnerConfig

Configuration for scoring, classifier setup, learning parameters, and optional features.

ErrorEstimationConfig

Configuration for global and local FDR (false discovery rate) estimation.

IPF Configuration

IPFIOConfig

Configuration for Inference of Peptidoforms (IPF).

Levels Context Configuration

LevelContextIOConfig

Configuration for level-based context inference (e.g., peptide, protein, gene, glycopeptide) with FDR estimation and visualization options.

Export Configuration

ExportIOConfig

Configuration for exporting results to various formats.