main

Main entry point for pod5 tools

main

main() -> Any

The core pod5 tools function which assembles the argparser and executes the required pod5 tool.

Parsers

Parsers for pod5 tools.

Each parser should have set_defaults(func=tool) called where tool is the core function of a pod5 tool. These are commonly tool_pod5 (e.g. subset_pod5, merge_pod5)

SubcommandHelpFormatter

Bases: RawDescriptionHelpFormatter, ArgumentDefaultsHelpFormatter

Helper function to prettier print subcommand help. This removes some extra lines of output when a final command parser is not selected.

pod5_convert_from_fast5_argparser

pod5_convert_from_fast5_argparser(
    parent: Optional[_SubParsersAction] = None,
) -> ArgumentParser

Create an argument parser for the pod5 convert-from-fast5 tool

pod5_convert_to_fast5_argparser

pod5_convert_to_fast5_argparser(
    parent: Optional[_SubParsersAction] = None,
) -> ArgumentParser

Create an argument parser for the pod5 convert-to-fast5 tool

prepare_pod5_convert

prepare_pod5_convert(parent: _SubParsersAction) -> ArgumentParser

Create an argument paraser for the pod5 convert entry point

prepare_pod5_filter_argparser

prepare_pod5_filter_argparser(
    parent: Optional[_SubParsersAction] = None,
) -> ArgumentParser

Create an argument parser for the pod5 filter tool

prepare_pod5_inspect_argparser

prepare_pod5_inspect_argparser(
    parent: Optional[_SubParsersAction] = None,
) -> ArgumentParser

Create an argument parser for the pod5 inspect tool

prepare_pod5_merge_argparser

prepare_pod5_merge_argparser(
    parent: Optional[_SubParsersAction] = None,
) -> ArgumentParser

Create an argument parser for the pod5 merge tool

prepare_pod5_recover_argparser

prepare_pod5_recover_argparser(
    parent: Optional[_SubParsersAction] = None,
) -> ArgumentParser

Create an argument parser for the pod5 recover tool

prepare_pod5_repack_argparser

prepare_pod5_repack_argparser(
    parent: Optional[_SubParsersAction] = None,
) -> ArgumentParser

Create an argument parser for the pod5 repack tool

prepare_pod5_subset_argparser

prepare_pod5_subset_argparser(
    parent: Optional[_SubParsersAction] = None,
) -> ArgumentParser

Create an argument parser for the pod5 subset tool

prepare_pod5_update_argparser

prepare_pod5_update_argparser(
    parent: Optional[_SubParsersAction] = None,
) -> ArgumentParser

Create an argument parser for the pod5 update tool

prepare_pod5_view_argparser

prepare_pod5_view_argparser(
    parent: Optional[_SubParsersAction] = None,
) -> ArgumentParser

Create an argument parser for the pod5 view tool

run_tool

run_tool(parser: ArgumentParser) -> Any

Run the tool prepared by an argparser