ample.util.argparse_util module

class BoolAction(option_strings, dest, nargs=None, const=None, default=None, type=None, choices=None, required=False, help=None, metavar=None)[source]

Bases: argparse.Action

Class to set a boolean value either form a string or just from the use of the command-line flag

class FilePathAction(option_strings, dest, nargs=None, const=None, default=None, type=None, choices=None, required=False, help=None, metavar=None)[source]

Bases: argparse.Action

Class to handle paths to files or directories.

AMPLE changes directory into a work directory so relative paths to files don’t work. We set absolulte paths here.

add_cluster_submit_options(parser=None)[source]

Add the options for submission to a cluster queuing system

add_contact_options(parser=None)[source]

Contact prediction related options

add_core_options(parser=None)[source]

Function to add any arguments required by all runtypes

add_ensembler_options(parser=None)[source]
add_general_options(parser=None)[source]
add_mr_options(parser=None)[source]
add_rosetta_options(parser=None)[source]
process_command_line(args=None, contacts=True, modelling=True, mol_rep=True)[source]

Process the command-line for the main AMPLE program. :args: optional argument that can hold the command-line arguments if we have been called from within python for testing