tracts.driver_utils

Functions

_get_display_param_indices(...[, steps])	Compute which parameter columns should be shown in starting-parameter tables.
_get_optimization_subtitle(...[, steps])	Build the user-readable optimization subtitle for the active run phase.
_normalize_multi_init_result(result)	Normalize outputs from multi-initialization optimization runs.
_print_run_intro(parameter_handler, model, ...)	Print the optimization subtitle and starting-parameter table for a run.
_print_step_header_block(parameter_handler)	Print starting-parameter information before optimization runs begin.
_summarize_step_results(params_found, ...[, ...])	Print per-run optimization results and select the best run.
collapse_identical_start_params(...)	Collapse repeated identical starting-parameter sets to a single repetition.
get_time_scaled_model_bounds(model[, verbose])	Computes a function that takes in optimizer parameters, converts them to physical parameters using the model's parameter handler, and returns the violation score for those parameters.
get_time_scaled_model_func(model)	Computes a function that takes in optimizer parameters, converts them to physical parameters using the model's parameter handler, and returns the migration matrices for those parameters.
load_driver_file(driver_path)	Loads the driver file and validates that it contains all required parameters for the inference.
load_model_from_driver(driver_spec, ...[, ...])	Loads the demographic model based on the specifications in the driver file.
load_population(driver_path, driver_spec[, ...])	Loads the population data based on the specifications in the driver file.
locate_file_path(filename, script_dir[, ...])	Locates the file path for a given filename by searching in multiple locations.
output_simulation_data_sex_biased(...[, ...])	Creates output graphs to compare data and the theoretical tract length distribution inferred by the model.
parse_chromosomes(chromosome_spec[, chromosomes])	Parses a chromosome specification and returns a list of chromosome numbers.
parse_individual_filenames(individual_names, ...)	Parses the individual filenames based on the provided format and locates their paths.
parse_start_params(start_param_bounds, model)	Produces starting parameters for optimization in physical units.
scale_select_indices(arr, indices_to_scale)

Classes

InferenceConfig(**data)	Configuration for the inference process.
SamplesConfig(**data)	Configuration for the samples used in the inference.
StartParamsConfig(**data)	Configuration for the starting parameters used in the optimization.