search_step

The search_step module organizes the search schedule for searching multiple files.

class alphadia.search_step.SearchStep(output_folder: str, config: dict | Config | None = None, cli_config: dict | None = None, extra_config: dict | None = None, step_name: str | None = None)[source]

Bases: object

__init__(output_folder: str, config: dict | Config | None = None, cli_config: dict | None = None, extra_config: dict | None = None, step_name: str | None = None) → None[source]

Highest level class to plan a DIA search step.

Owns the input file list, speclib and the config. Performs required manipulation of the spectral library like transforming RT scales and adding columns.

Parameters:

  • output_folder (str) – output folder to save the results

  • config (dict, optional) – values to update the default config. Overrides values in default.yaml.

  • cli_config (dict, optional) – additional config values (parameters from the command line). Overrides values in config.

  • extra_config (dict, optional) – additional config values (parameters to orchestrate multistep searches). Overrides values in config and cli_config.

property config: Config

Dict with all configuration parameters for the extraction.

load_library()[source]

Load or build spectral library as configured.

Steps 1 to 3 are performed depending on the quality and information in the spectral library. Step 4 is always performed to prepare the library for search.

run() → list[tuple[str, str]][source]

Run the search step.

This has three main parts: 1. Load or build the spectral library 2. Iterate over all raw files and perform the search workflow 3. Collect and summarize the results

Returns:

List of tuples containing (step_name, raw_file_name) for files that encountered errors during processing.

Return type:

list of tuples

property spectral_library: SpecLibFlat

Flattened Spectral Library.