def main_cli(): description = '{name} {version}'.format(**_program_info) parser = argparse.ArgumentParser(description=description) parser.add_argument('div_model_path', metavar='DIV-MODEL-RESULTS-FILE', type=argparse_utils.arg_is_file, help=('Path to divergence model results file (i.e., ' '`*-div-model-results.txt`).')) parser.add_argument( '-i', '--taxon-indices', nargs='+', type=argparse_utils.arg_is_positive_int, required=True, help=('Two or more space-separated indices of taxa for which to ' 'calculate the probability of them co-diverging. Indices ' 'correspond to the line in the sample table of the config, ' 'starting at 1 for the first line of the table. At least ' 'two indices are required.')) parser.add_argument( '-c', '--config', type=argparse_utils.arg_is_config, help=('msBayes config file to be used to estimate prior ' 'probability via simulations. If provided, the ' 'posterior and prior probability and bayes factor is ' 'reported. If not provided, only the posterior ' 'probability is reported.')) parser.add_argument( '-n', '--num-prior-samples', action='store', type=argparse_utils.arg_is_positive_int, default=100000, help=('The number of prior samples to simulate for estimating' 'prior probabilities. Only used if a config file is ' 'provided with the `-c` argument.')) parser.add_argument( '--np', action='store', type=argparse_utils.arg_is_positive_int, default=multiprocessing.cpu_count(), help=('The maximum number of processes to run in parallel for ' 'prior simulations. The default is the number of CPUs ' 'available on the machine. This option is only relevant ' 'if a config file is provided using the `-c` argument.')) parser.add_argument( '--seed', action='store', type=argparse_utils.arg_is_positive_int, help=('Random number seed to use for simulations. This option ' 'is only relevant if a config file is provided using the ' '`-c` argument.')) parser.add_argument('--version', action='version', version='%(prog)s ' + _program_info['version'], help='Report version and exit.') parser.add_argument('--quiet', action='store_true', help='Run without verbose messaging.') parser.add_argument('--debug', action='store_true', help='Run in debugging mode.') args = parser.parse_args() ########################################################################## ## handle args from pymsbayes.utils.messaging import (LoggingControl, InfoLogger) LoggingControl.set_logging_level("INFO") if args.quiet: LoggingControl.set_logging_level("WARNING") if args.debug: LoggingControl.set_logging_level("DEBUG") log = LoggingControl.get_logger(__name__) from pymsbayes import config from pymsbayes.teams import ModelProbabilityEstimatorTeam from pymsbayes.utils import sumresults, GLOBAL_RNG if len(args.taxon_indices) < 2: log.error('At least two taxon indices are required') sys.exit(1) if not args.seed: args.seed = random.randint(1, 999999999) GLOBAL_RNG.seed(args.seed) div_models = sumresults.OrderedDivergenceModelCollection( div_model_results_path=args.div_model_path) for i in args.taxon_indices: if ((i < 1) or (i > div_models.npairs)): log.error('taxon index {0} is out of bounds'.format(i)) sys.exit(1) args.taxon_indices = [i - 1 for i in args.taxon_indices] prob_shared_div = div_models.prob_of_shared_divergence(args.taxon_indices) if args.config: prob_estimator_team = ModelProbabilityEstimatorTeam( config_paths=[args.config], num_samples=args.num_prior_samples, num_processors=args.np) prob_estimator_team.start() prior_prob = prob_estimator_team.shared_div_probs[args.config][len( args.taxon_indices)] bf = ((prob_shared_div / (1 - prob_shared_div)) / (prior_prob / (1 - prior_prob))) sys.stdout.write('posterior probability = {0}\n'.format(prob_shared_div)) if args.config: sys.stdout.write('prior probability = {0}\n'.format(prior_prob)) sys.stdout.write('Bayes factor = {0}\n'.format(bf)) sys.stdout.write('2ln(Bayes factor) = {0}\n'.format(2 * math.log(bf)))
def main_cli(): description = '{name} {version}'.format(**_program_info) parser = argparse.ArgumentParser(description=description) parser.add_argument( 'configs', metavar='CONFIG-PATH', type=arg_is_config, nargs='+', help=('msBayes config file paths for which to estimate prior ' 'probabilities.')) parser.add_argument('-n', '--num-prior-samples', action='store', type=int, default=1000, help=('The number of prior samples to simulate for ' 'proabability estimates.')) parser.add_argument( '--np', action='store', type=int, default=multiprocessing.cpu_count(), help=('The maximum number of processes to run in parallel. The ' 'default is the number of CPUs available on the machine.')) parser.add_argument( '-d', '--dispersion-threshold', action='store', type=float, default=0.01, help=('The threshold for the dispersion index of divegence ' 'times. The estimated prior probability that the ' 'dispersion index is less than this threshold will ' 'be reported for each config.')) parser.add_argument( '-c', '--cv-threshold', action='store', type=float, default=0.01, help=('The threshold for the coefficient of variation (CV) of ' 'divegence times. The estimated prior probability that the ' 'CV is less than this threshold will ' 'be reported for each config.')) parser.add_argument('--seed', action='store', type=int, help='Random number seed to use for the analysis.') parser.add_argument('--version', action='version', version='%(prog)s ' + _program_info['version'], help='Report version and exit.') parser.add_argument('--quiet', action='store_true', help='Run without verbose messaging.') parser.add_argument('--debug', action='store_true', help='Run in debugging mode.') args = parser.parse_args() ########################################################################## ## handle args from pymsbayes.utils.messaging import (LoggingControl, InfoLogger) LoggingControl.set_logging_level("INFO") if args.quiet: LoggingControl.set_logging_level("WARNING") if args.debug: LoggingControl.set_logging_level("DEBUG") log = LoggingControl.get_logger(__name__) from pymsbayes.teams import ModelProbabilityEstimatorTeam from pymsbayes.utils import GLOBAL_RNG if not args.seed: args.seed = random.randint(1, 999999999) log.info('Using seed {0}'.format(args.seed)) GLOBAL_RNG.seed(args.seed) ########################################################################## ## begin analysis --- generate samples start_time = datetime.datetime.now() prob_esimator_team = ModelProbabilityEstimatorTeam( config_paths=args.configs, num_samples=args.num_prior_samples, omega_threshold=args.dispersion_threshold, cv_threshold=args.cv_threshold, num_processors=args.np) prob_esimator_team.start() for path in args.configs: sys.stdout.write('Prior probabilities for model {0}:\n'.format(path)) for k, p in prob_esimator_team.psi_probs[path].iteritems(): sys.stdout.write('\tnum of divergence events = {0}: {1}\n'.format( k, p)) sys.stdout.write('\tdispersion of div times < {0}: {1}\n'.format( args.dispersion_threshold, prob_esimator_team.omega_probs[path])) sys.stdout.write('\tCV of div times < {0}: {1}\n'.format( args.cv_threshold, prob_esimator_team.cv_probs[path])) stop_time = datetime.datetime.now() log.info('[run_stats]') log.info('\tstart_time = {0}'.format(str(start_time))) log.info('\tstop_time = {0}'.format(str(stop_time))) log.info('\ttotal_duration = {0}'.format(str(stop_time - start_time)))
def main_cli(): description = '{name} {version}'.format(**_program_info) parser = argparse.ArgumentParser(description = description) parser.add_argument('div_model_path', metavar='DIV-MODEL-RESULTS-FILE', type=argparse_utils.arg_is_file, help = ('Path to divergence model results file (i.e., ' '`*-div-model-results.txt`).')) parser.add_argument('-i', '--taxon-indices', nargs = '+', type = argparse_utils.arg_is_positive_int, required = True, help = ('Two or more space-separated indices of taxa for which to ' 'calculate the probability of them co-diverging. Indices ' 'correspond to the line in the sample table of the config, ' 'starting at 1 for the first line of the table. At least ' 'two indices are required.')) parser.add_argument('-c', '--config', type = argparse_utils.arg_is_config, help = ('msBayes config file to be used to estimate prior ' 'probability via simulations. If provided, the ' 'posterior and prior probability and bayes factor is ' 'reported. If not provided, only the posterior ' 'probability is reported.')) parser.add_argument('-n', '--num-prior-samples', action = 'store', type = argparse_utils.arg_is_positive_int, default = 100000, help = ('The number of prior samples to simulate for estimating' 'prior probabilities. Only used if a config file is ' 'provided with the `-c` argument.')) parser.add_argument('--np', action = 'store', type = argparse_utils.arg_is_positive_int, default = multiprocessing.cpu_count(), help = ('The maximum number of processes to run in parallel for ' 'prior simulations. The default is the number of CPUs ' 'available on the machine. This option is only relevant ' 'if a config file is provided using the `-c` argument.')) parser.add_argument('--seed', action = 'store', type = argparse_utils.arg_is_positive_int, help = ('Random number seed to use for simulations. This option ' 'is only relevant if a config file is provided using the ' '`-c` argument.')) parser.add_argument('--version', action = 'version', version = '%(prog)s ' + _program_info['version'], help = 'Report version and exit.') parser.add_argument('--quiet', action = 'store_true', help = 'Run without verbose messaging.') parser.add_argument('--debug', action = 'store_true', help = 'Run in debugging mode.') args = parser.parse_args() ########################################################################## ## handle args from pymsbayes.utils.messaging import (LoggingControl, InfoLogger) LoggingControl.set_logging_level("INFO") if args.quiet: LoggingControl.set_logging_level("WARNING") if args.debug: LoggingControl.set_logging_level("DEBUG") log = LoggingControl.get_logger(__name__) from pymsbayes import config from pymsbayes.teams import ModelProbabilityEstimatorTeam from pymsbayes.utils import sumresults, GLOBAL_RNG if len(args.taxon_indices) < 2: log.error('At least two taxon indices are required') sys.exit(1) if not args.seed: args.seed = random.randint(1, 999999999) GLOBAL_RNG.seed(args.seed) div_models = sumresults.OrderedDivergenceModelCollection( div_model_results_path = args.div_model_path) for i in args.taxon_indices: if ((i < 1) or (i > div_models.npairs)): log.error('taxon index {0} is out of bounds'.format(i)) sys.exit(1) args.taxon_indices = [i - 1 for i in args.taxon_indices] prob_shared_div = div_models.prob_of_shared_divergence(args.taxon_indices) if args.config: prob_estimator_team = ModelProbabilityEstimatorTeam( config_paths = [args.config], num_samples = args.num_prior_samples, num_processors = args.np) prob_estimator_team.start() prior_prob = prob_estimator_team.shared_div_probs[args.config][ len(args.taxon_indices)] bf = ((prob_shared_div / (1 - prob_shared_div)) / (prior_prob / (1 - prior_prob))) sys.stdout.write('posterior probability = {0}\n'.format(prob_shared_div)) if args.config: sys.stdout.write('prior probability = {0}\n'.format(prior_prob)) sys.stdout.write('Bayes factor = {0}\n'.format(bf)) sys.stdout.write('2ln(Bayes factor) = {0}\n'.format(2 * math.log(bf)))