ample.util.argparse_util module¶

Below is code for creating a boolean argument parser with a default, and a range of choices

class BoolAction(argparse.Action):

def __call__(self, parser, namespace, values, option_string=None):

if values is None: values = self.default if values in [ ‘0’, ‘f’, ‘F’, ‘false’, ‘False’, False ]:

values=False

elif values in [ ‘1’, ‘t’, ‘T’, ‘true’, ‘True’, True ]:

values=True

else:

msg = ‘Unrecognised True/False value: {0}’.format(values) raise argparse.ArgumentError(self, msg)

setattr(namespace, self.dest, values)

parser = argparse.ArgumentParser()

parser.add_argument(‘-d’, ‘–debug’, action=BoolAction, default=True, metavar=’True/False’, nargs=’?’, help=”debug”) # print(parser.parse_args(‘-d 2’.split())) print(parser.parse_args(‘-d false’.split()))

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_general_options(parser=None)[source]¶

add_mr_options(parser=None)[source]¶

add_rosetta_options(parser=None)[source]¶