deeprvat.deeprvat.config

Module Contents

Functions

cli

setup_logging

load_yaml

update_defaults

Updates base_config with values from input_config, for intersecting nested keys.

handle_cv_options

handle_regenie_options

handle_pretrained_models

update_thresholds

update_full_config

validate_keys

create_main_config

Generates the necessary deeprvat_config.yaml file for running all pipelines. This function expects inputs as shown in the following config-file: - DEEPRVAT_DIR/example/deeprvat_input_config.yaml

create_sg_discovery_config

Generates the necessary sg_discovery_config.yaml file for running the seed_gene_discovery pipelines. This function expects inputs as shown in the following config-file: - DEEPRVAT_DIR/example/seed_gene_discovery_input_config.yaml

update_config

Select seed genes based on baseline results and update the configuration file.

Data

REPO_DIR

logger

API

deeprvat.deeprvat.config.REPO_DIR = 'resolve(...)'
deeprvat.deeprvat.config.logger = 'getLogger(...)'
deeprvat.deeprvat.config.cli()
deeprvat.deeprvat.config.setup_logging(log_filename: str = 'config_generate.log')
deeprvat.deeprvat.config.load_yaml(file_path: str)
deeprvat.deeprvat.config.update_defaults(base_config, input_config)

Updates base_config with values from input_config, for intersecting nested keys.

Args:

base_config (dict): base DeepRVAT configurations input_config (dict): user input DeepRVAt configurations

Returns:

dict: updated base_config based on any intersecting inputs from input_config

deeprvat.deeprvat.config.handle_cv_options(input_config, full_config, expected_input_keys)
deeprvat.deeprvat.config.handle_regenie_options(input_config, full_config, expected_input_keys)
deeprvat.deeprvat.config.handle_pretrained_models(input_config, expected_input_keys)
deeprvat.deeprvat.config.update_thresholds(input_config, full_config, train_only)
deeprvat.deeprvat.config.update_full_config(input_config, full_config, train_only)
deeprvat.deeprvat.config.validate_keys(input_config, expected_input_keys, optional_input_keys, base_config)
deeprvat.deeprvat.config.create_main_config(config_file: str, output_dir: Optional[str] = '.', clobber: Optional[bool] = False)

Generates the necessary deeprvat_config.yaml file for running all pipelines. This function expects inputs as shown in the following config-file: - DEEPRVAT_DIR/example/deeprvat_input_config.yaml

Parameters:

  • config_file (str) – Path to directory of relevant config yaml file

  • output_dir (str) – Path to directory where created deeprvat_config.yaml will be saved.

  • clobber (bool) – Overwrite existing deeprvat_config.yaml, even if it is newer than config_file

Returns:

Joined configuration file saved to deeprvat_config.yaml.

deeprvat.deeprvat.config.create_sg_discovery_config(config_file: str, output_dir: Optional[str] = '.')

Generates the necessary sg_discovery_config.yaml file for running the seed_gene_discovery pipelines. This function expects inputs as shown in the following config-file: - DEEPRVAT_DIR/example/seed_gene_discovery_input_config.yaml

Parameters:

  • config_file (str) – Path to directory of relevant config yaml file

  • output_dir (str) – Path to directory where created sg_discovery_config.yaml will be saved.

Returns:

Joined configuration file saved to sg_discovery_config.yaml.

deeprvat.deeprvat.config.update_config(association_only: bool, phenotype: Optional[str], baseline_results: Tuple[str], baseline_results_out: Optional[str], seed_genes_out: Optional[str], old_config_file: str, new_config_file: str)

Select seed genes based on baseline results and update the configuration file.

Parameters:

  • association_only (bool) – Update config file only for association testing

  • old_config_file (str) – Path to the old configuration file.

  • phenotype (Optional[str]) – Phenotype to update in the configuration.

  • baseline_results (Tuple[str]) – Paths to baseline result files.

  • baseline_results_out (Optional[str]) – Path to save the updated baseline results.

  • seed_genes_out (Optional[str]) – Path to save the seed genes.

  • new_config_file (str) – Path to the new configuration file.

Raises:

ValueError – If neither –seed-gene-dir nor –baseline-results is specified.

Returns:

Updated configuration file saved to new_config.yaml. Selected seed genes saved to seed_genes_out.parquet. Optionally, save baseline results to a parquet file if baseline_results_out is specified.