API Overview

Modules

• abstract_classes: Package for ZARP-cli abstract classes.
• abstract_classes.sample_processor: Abstract sample processor classes.
• cli: Command-line interface client.
• config: Subpackage for handling ZARP-cli configuration.
• config.args: Command-line argument parser class.
• config.constants: Constants.
• config.enums: Configuration enumerators.
• config.init: Handle initialization mode.
• config.mappings: Mappings and lists for ZARP and ZARP-cli models and tables.
• config.models: Configuration models.
• config.parser: Configuration parser.
• config.sample_tables: ZARP sample table processing.
• config.samples: ZARP sample processing.
• plugins: Subpackage for ZARP-cli plugins.
• plugins.sample_dereferencers: Subpackage for ZARP-cli sample dereferencer plugins.
• plugins.sample_fetchers: Subpackage for ZARP-cli sample fetcher plugins.
• plugins.sample_fetchers.sra: Fetch remote samples from SRA.
• plugins.sample_processors: Subpackage for ZARP-cli sample processor plugins.
• plugins.sample_processors.defaults: Set missing metadata defaults.
• plugins.sample_processors.dummy_data: Fill in missing metadata with dummy data.
• plugins.sample_processors.genomepy: Fetch genome resources with mod:genomepy.
• plugins.sample_processors.htsinfer: Infer missing sample metadata with HTSinfer.
• runner: Subpackage for ZARP-cli runners.
• runner.zarp_runner: Infer missing sample metadata with HTSinfer.
• samples: Subpackage for ZARP sample-related classes and functions.
• samples.sample_record_processor: Interact with ZARP sample records.
• samples.sample_table_processor: Read and write ZARP sample tables.
• snakemake: Subpackage for ZARP-cli interaction with Snakemake.
• snakemake.config_file_processor: Snakemake config file processor.
• snakemake.run: Module for executing Snakemake workflows.
• utils: ZARP-cli utilities.
• version: Single source of truth for package version.
• zarp: Main class and entry point when imported as a library.

Classes

• sample_processor.SampleProcessor: Abstract sample processor class.
• args.ArgParser: ZARP-cli argument parser class.
• enums.DependencyEmbeddingStrategies: Supported dependency embedding strategies.
• enums.ExecModes: Execution modes.
• enums.FieldNameMappingDirection: Field name direction enumerator.
• enums.LogLevels: Log level enumerator.
• enums.ReadOrientation: Read orientation types.
• enums.SampleReferenceTypes: Types of sample references.
• enums.SnakemakeRunState: Snakemake run states.
• init.Initializer: Handler for app initialization.
• models.Config: ZARP-cli main configuration.
• models.ConfigFileContent: Snakemake configuration file content.
• models.ConfigFileHTSinfer: HTSinfer workflow configuration file content.
• models.ConfigFileSRA: SRA download workflow configuration file content.
• models.ConfigFileZARP: ZARP workflow configuration file content.
• models.ConfigRun: Run-specific parameters.
• models.ConfigSample: Sample-specific parameters.
• models.ConfigUser: User-specific parameters.
• models.CustomBaseModel: Base model that all other models derive from.
• models.InitConfig: ZARP-cli user default configuration set during initialization.
• models.InitRun: Run-specific parameters for initialization.
• models.InitSample: Sample-specific parameters for initialization.
• models.InitUser: User-specific parameters for initialization.
• models.Sample: Sample-specific parameters.
• models.SampleReference: Sample reference information.
• parser.ConfigParser: Configuration parser for ZARP-cli.
• sample_tables.SampleTableProcessor: Process ZARP sample tables.
• samples.SampleProcessor: Process ZARP samples.
• sra.SampleFetcherSRA: Fetch remote samples from SRA.
• defaults.SampleProcessorDefaults: Set available defaults for missing sample metadata.
• dummy_data.SampleProcessorDummyData: Set dummy data for missing sample metadata, as required by ZARP.
• genomepy.SampleProcessorGenomePy: Fetch genome resources with mod:genomepy.
• htsinfer.SampleProcessorHTSinfer: Infer metadata with HTSinfer.
• zarp_runner.SampleRunnerZARP: Infer metadata with HTSinfer.
• sample_record_processor.SampleRecordProcessor: ZARP sample record processor class.
• config_file_processor.ConfigFileProcessor: Write Snakemake configuration files.
• run.SnakemakeExecutor: Run snakemake with system calls.
• zarp.ZARP: Handle ZARP workflow execution.

Functions

• cli.main: Entry point for CLI executable.
• cli.setup_logging: Configure logging.
• sample_table_processor.read: Set records from sample table file.
• sample_table_processor.write: Write sample table.
• utils.generate_id: Generate random string.
• utils.list_get: Get an item from a list by index or return a default value.
• utils.remove_none: Remove None values from a (nested) dictionary.
• utils.resolve_paths: Resolve relative sample paths against a defined anchor.
• utils.sanitize_strings: Sanitize strings.