def parse_args():
"""
Parse the arguments.
Parse the command line arguments/options using the argparse module
and return the parsed arguments (as an argparse.Namespace object,
as returned by argparse.parse_args()).
Returns:
argparse.Namespace: the parsed arguments
"""
parser = argparse.ArgumentParser()
parser.add_argument('input_expression', type=str,
help='name of the file containg expression data')
parser.add_argument('input_response', type=str,
help='name of the file containg response data')
parser.add_argument('input_network', type=str,
help='name of the file containg network data')
parser.add_argument('-s', '--seed', type=int, default=1011,
help='seed used for random generator')
parser.add_argument('-pt', '--prob_restart_trans', type=float, default=0.5,
help='restart probability of RWR to network-transform expression')
parser.add_argument('-t', '--tolerance', type=float, default=1e-8,
help='tolerance used to determine convergence of RWR')
parser.add_argument('-mi', '--max_iteration', type=int, default=100,
help='maximum number of iterations used in RWR')
parser.add_argument('-nb', '--num_bootstrap', type=int, default=1,
help='number of bootstrap samplings')
parser.add_argument('-pb', '--percent_bootstrap', type=int, default=100,
help='percent of samples for bootstrap samplinga (between 0-100)')
parser.add_argument('-de', '--directory_expression', type=str,
default='./',
help='directory containing expression data')
parser.add_argument('-dr', '--directory_response', type=str,
default='./',
help='directory containing response data')
parser.add_argument('-dn', '--directory_network', type=str,
default='./',
help='directory containing network data')
parser.add_argument('-do', '--directory_out', type=str,
default='./',
help='directory for the results')
parser.add_argument('-o', '--output', type=str,
default='results.csv',
help='name of the file containg the results')
args = parser.parse_args()
return args
###############################################################################
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