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)