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)

class SubcommandHelpFormatter(prog, indent_increment=2, max_help_position=24, width=None)

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.

add_force_overwrite_argument(parser: _ActionsContainer)

add_recursive_argument(parser: ArgumentParser)

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(parent: Optional[_SubParsersAction] = None) → ArgumentParser

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

prepare_pod5_convert(parent: _SubParsersAction) → ArgumentParser

Create an argument paraser for the pod5 convert entry point

prepare_pod5_filter_argparser(parent: Optional[_SubParsersAction] = None) → ArgumentParser

Create an argument parser for the pod5 filter tool

prepare_pod5_inspect_argparser(parent: Optional[_SubParsersAction] = None) → ArgumentParser

Create an argument parser for the pod5 inspect tool

prepare_pod5_merge_argparser(parent: Optional[_SubParsersAction] = None) → ArgumentParser

Create an argument parser for the pod5 merge tool

prepare_pod5_recover_argparser(parent: Optional[_SubParsersAction] = None) → ArgumentParser

Create an argument parser for the pod5 recover tool

prepare_pod5_repack_argparser(parent: Optional[_SubParsersAction] = None) → ArgumentParser

Create an argument parser for the pod5 repack tool

prepare_pod5_subset_argparser(parent: Optional[_SubParsersAction] = None) → ArgumentParser

Create an argument parser for the pod5 subset tool

prepare_pod5_update_argparser(parent: Optional[_SubParsersAction] = None) → ArgumentParser

Create an argument parser for the pod5 update tool

prepare_pod5_view_argparser(parent: Optional[_SubParsersAction] = None) → ArgumentParser

Create an argument parser for the pod5 view tool

run_tool(parser: ArgumentParser) → Any

Run the tool prepared by an argparser