dynast.main

Module Contents

Functions

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

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

Return type

argparse.ArgumentParser

dynast.main.setup_align_args(parser, parent)

dynast.main.setup_consensus_args(parser, parent)

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

Return type

argparse.ArgumentParser

dynast.main.setup_count_args(parser, parent)

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

Return type

argparse.ArgumentParser

dynast.main.setup_estimate_args(parser, parent)

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

Return type

argparse.ArgumentParser

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

Parser for the ref command. :param args: Command-line arguments dictionary, as parsed by argparse :type args: dict

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

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

Parser for the consensus command. :param args: Command-line arguments dictionary, as parsed by argparse :type args: dict

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

Parser for the count command. :param args: Command-line arguments dictionary, as parsed by argparse :type args: dict

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

dynast.main.COMMAND_TO_FUNCTION

dynast.main.main()