def main(num_ranks, num_simulations): for i in range(1, num_ranks + 1): dir_name = "from_subtree_{i}".format(i=i) os.makedirs(dir_name) os.chdir(dir_name) mylogger.initialize(dir_name) prune_subtrees(i, ALIGN, num_simulations) os.chdir("../")
parser.add_argument('--trimal_gapthreshold', '-trimal', required=False, default=-1, help='gapthreshold of trimal') parser.add_argument('--num_simulations', '-n', required=True, help='number of simulations') args = parser.parse_args() species_list = args.species_list output_name = args.output_name num_simulations = int(args.num_simulations) trimal_gapthreshold = float(args.trimal_gapthreshold) mylogger.initialize(output_name) logging.info("species list: {}".format(species_list)) logging.info("output name: {}".format(output_name)) logging.info("number of simulations: {}".format(num_simulations)) logging.info( "indelible sequences - alinged: {}".format(INDELIBLE_SEQS_ALIGNED)) logging.info("indelible sequences - not alinged: {}".format( INDELIBLE_SEQS_UNALIGNED)) logging.info("genes: {}".format(", ".join(GENES))) logging.info("gapthreshold of trimal: {}".format(trimal_gapthreshold)) main(species_list, output_name, num_simulations, trimal_gapthreshold)
parser.add_argument('-max_gaps', '-max', required=False, default=50, help='max gaps for indelible control file') parser.add_argument('-output', '-o', required=False, default=OUTPUT, help='output name of final file') parser.add_argument('-paths', action='store_true', help='file contains paths') args = parser.parse_args() mylogger.initialize("fit_indel_parameters_logfile.csv") logging.info("gene name:,{}".format(args.gene)) logging.info("model file:,{}".format(args.model_file)) logging.info("tree file:,{}".format(args.tree_file)) logging.info("num simulations:,{}".format(args.n)) logging.info("reference alignment:,{}".format(args.ref)) logging.info("max gaps length:,{}".format(args.ref)) logging.info("range divided to: {}".format(INTERVALS)) if args.paths: main_paths(args.gene, args.model_file, args.tree_file, args.n, args.ref, args.max_gaps, args.output) else: main(args.gene, args.model_file, args.tree_file, args.n, args.ref, args.max_gaps, args.output)
i += 1 def main(): logging.info("true tree: " + TRUE_TREE) logging.info("small tree speicies: " + SMALL_TEEE_SPECIES) logging.info("big tree speicies: " + BIG_TEEE_SPECIES) small_species = read_species(SMALL_TEEE_SPECIES) big_species = read_species(BIG_TEEE_SPECIES) logging.info("# species in small tree: " + str(len(small_species))) logging.info("# species in big tree: " + str(len(big_species))) species_in_big_only = [ species for species in big_species if species not in small_species ] lion_in_desert2(small_species, species_in_big_only) if __name__ == "__main__": if len(sys.argv) < 1: print "please insert argument" sys.exit(0) mylogger.initialize(__file__) main()
os.chdir("../") if __name__ == "__main__": parser = argparse.ArgumentParser(description='') parser.add_argument('--ranks', '-r', required=True, help='number of ranks in tree') parser.add_argument('--simulations', '-n', required=True, help='number of simulations') args = parser.parse_args() num_ranks = int(args.ranks) num_simulations = int(args.simulations) mylogger.initialize("prune_subtrees.logfile") logging.info("num ranks: {}".format(num_ranks)) logging.info("number of simulations: {}".format(num_simulations)) logging.info("paths of trees: {}".format(TREE_PATH)) logging.info("paths of species: {}".format(SPECIES_PATH)) logging.info("alignments aligned by: {}".format(ALIGN)) main(num_ranks, num_simulations)