dynast.main

Module Contents

Functions

print_technologies()	Displays a list of supported technologies along with whether a whitelist
setup_ref_args(parser: argparse.ArgumentParser, parent: argparse.ArgumentParser) → argparse.ArgumentParser	Helper function to set up a subparser for the ref command.
setup_align_args(parser: argparse.ArgumentParser, parent: argparse.ArgumentParser) → argparse.ArgumentParser	Helper function to set up a subparser for the align command.
setup_consensus_args(parser: argparse.ArgumentParser, parent: argparse.ArgumentParser) → argparse.ArgumentParser	Helper function to set up a subparser for the consensus command.
setup_count_args(parser: argparse.ArgumentParser, parent: argparse.ArgumentParser) → argparse.ArgumentParser	Helper function to set up a subparser for the count command.
setup_estimate_args(parser: argparse.ArgumentParser, parent: argparse.ArgumentParser) → argparse.ArgumentParser	Helper function to set up a subparser for the estimate command.
parse_ref(parser: argparse.ArgumentParser, args: argparse.Namespace, temp_dir: Optional[str] = None)	Parser for the ref command.
parse_align(parser, args, temp_dir=None)
parse_consensus(parser: argparse.ArgumentParser, args: argparse.Namespace, temp_dir: Optional[str] = None)	Parser for the consensus command.
parse_count(parser: argparse.ArgumentParser, args: argparse.Namespace, temp_dir: Optional[str] = None)	Parser for the count command.
parse_estimate(parser: argparse.ArgumentParser, args: argparse.Namespace, temp_dir: Optional[str] = None)	Parser for the estimate command.
main()

Attributes

COMMAND_TO_FUNCTION

dynast.main.print_technologies()

Displays a list of supported technologies along with whether a whitelist is provided for that technology.

dynast.main.setup_ref_args(parser: argparse.ArgumentParser, parent: argparse.ArgumentParser) → argparse.ArgumentParser

Helper function to set up a subparser for the ref command.

Parameters

parser

Argparse parser to add the ref command to

parent

Argparse parser parent of the newly added subcommand. Used to inherit shared commands/flags

Returns

The newly added parser

dynast.main.setup_align_args(parser: argparse.ArgumentParser, parent: argparse.ArgumentParser) → argparse.ArgumentParser

Helper function to set up a subparser for the align command.

Parameters

parser

Argparse parser to add the align command to

parent

Argparse parser parent of the newly added subcommand. Used to inherit shared commands/flags

Returns

The newly added parser

dynast.main.setup_consensus_args(parser: argparse.ArgumentParser, parent: argparse.ArgumentParser) → argparse.ArgumentParser

Helper function to set up a subparser for the consensus command.

Parameters

parser

Argparse parser to add the consensus command to

parent

Argparse parser parent of the newly added subcommand. Used to inherit shared commands/flags

Returns

The newly added parser

dynast.main.setup_count_args(parser: argparse.ArgumentParser, parent: argparse.ArgumentParser) → argparse.ArgumentParser

Helper function to set up a subparser for the count command.

Parameters

parser

Argparse parser to add the count command to

parent

Argparse parser parent of the newly added subcommand. Used to inherit shared commands/flags

Returns

The newly added parser

dynast.main.setup_estimate_args(parser: argparse.ArgumentParser, parent: argparse.ArgumentParser) → argparse.ArgumentParser

Helper function to set up a subparser for the estimate command.

Parameters

parser

Argparse parser to add the estimate command to

parent

Argparse parser parent of the newly added subcommand. Used to inherit shared commands/flags

Returns

The newly added parser

dynast.main.parse_ref(parser: argparse.ArgumentParser, args: argparse.Namespace, temp_dir: Optional[str] = None)

Parser for the ref command.

Parameters

parser

The parser

args

Command-line arguments dictionary, as parsed by argparse

temp_dir

Temporary directory

dynast.main.parse_align(parser, args, temp_dir=None)

dynast.main.parse_consensus(parser: argparse.ArgumentParser, args: argparse.Namespace, temp_dir: Optional[str] = None)

Parser for the consensus command.

Parameters

parser

The parser

args

Command-line arguments dictionary, as parsed by argparse

temp_dir

Temporary directory

dynast.main.parse_count(parser: argparse.ArgumentParser, args: argparse.Namespace, temp_dir: Optional[str] = None)

Parser for the count command.

Parameters

parser

The parser

args

Command-line arguments dictionary, as parsed by argparse

temp_dir

Temporary directory

dynast.main.parse_estimate(parser: argparse.ArgumentParser, args: argparse.Namespace, temp_dir: Optional[str] = None)

Parser for the estimate command.

Parameters

parser

The parser

args

Command-line arguments dictionary, as parsed by argparse

temp_dir

Temporary directory

dynast.main.COMMAND_TO_FUNCTION

dynast.main.main()