def main(args):
paralog1 = 'YDR418W'
paralog2 = 'YEL054C'
paralog = [paralog1, paralog2]
newicktree = './YeastTree.newick'
IGC_geo = args.IGC_geo
sim_num = args.sim_num
alignment_file = './' + '_'.join(paralog) + '/IGCgeo_' + str(IGC_geo) + '/sim_' + str(sim_num) + '/' + '_'.join(paralog) + '_MG94_geo_' + str(IGC_geo) + '_Sim_' + str(sim_num) + '.fasta'
save_name = './SimulationSave/' + '_'.join(paralog) + '/IGCgeo_' + str(IGC_geo) + '/' + '_'.join(paralog) + '_MG94_geo_' + str(IGC_geo) + '_Sim_' + str(sim_num) + '_save.txt'
summary_name = './SimulationSummary/' + '_'.join(paralog) + '/IGCgeo_' + str(IGC_geo) + '/' + '_'.join(paralog) + '_MG94_geo_' + str(IGC_geo) + '_Sim_' + str(sim_num) + '_summary.txt'
# generate folder if not exist
if not os.path.isdir('./SimulationSave/' + '_'.join(paralog) + '/'):
os.mkdir('./SimulationSave/' + '_'.join(paralog) + '/')
if not os.path.isdir('./SimulationSave/' + '_'.join(paralog) + '/IGCgeo_' + str(IGC_geo) + '/'):
os.mkdir('./SimulationSave/' + '_'.join(paralog) + '/IGCgeo_' + str(IGC_geo) + '/')
if not os.path.isdir('./SimulationSummary/' + '_'.join(paralog) + '/'):
os.mkdir('./SimulationSummary/' + '_'.join(paralog) + '/')
if not os.path.isdir('./SimulationSummary/' + '_'.join(paralog) + '/IGCgeo_' + str(IGC_geo) + '/'):
os.mkdir('./SimulationSummary/' + '_'.join(paralog) + '/IGCgeo_' + str(IGC_geo) + '/')
test = ReCodonGeneconv( newicktree, alignment_file, paralog, Model = 'MG94', Force = None, clock = False, save_name = save_name)
test.get_mle(False, True, 0, 'BFGS')
test.get_individual_summary(summary_path = './SimulationSummary/' + '_'.join(paralog) + '/', file_name = summary_name)
def main(args):
paralog = [args.paralog1, args.paralog2]
Force = None
clock = False
alignment_file = "./GeneFamilies/" + "_".join(paralog) + "/" + "_".join(paralog) + "_input.fasta"
newicktree = "./YeastTree.newick"
if args.force:
if model == "MG94":
Force = {5: 0.0}
elif model == "HKY":
Force = {4: 0.0}
else:
Force = None
test = ReCodonGeneconv(newicktree, alignment_file, paralog, Model=args.model, Force=Force, clock=args.clock)
test.get_mle(True, True, 0, "BFGS")
test.get_individual_summary(summary_path="./Summary/")
def main(args):
paralog = [args.paralog1, args.paralog2]
Force = None
clock = False
alignment_file = '../IdenticalParalogAlignment/' + '_'.join(paralog) + '/' + '_'.join(paralog) + '_IdenticalParalog_input.fasta'
newicktree = './YeastTree.newick'
if args.force:
if model == 'MG94':
Force = {5:0.0}
elif model == 'HKY':
Force = {4:0.0}
else:
Force = None
test = ReCodonGeneconv( newicktree, alignment_file, paralog, Model = args.model, Force = Force, clock = args.clock)
test.get_mle(True, True, 0, 'BFGS')
test.get_individual_summary(summary_path = './Summary/')
def main(args):
paralog1 = 'YDR418W'
paralog2 = 'YEL054C'
paralog = [paralog1, paralog2]
newicktree = './YeastTree.newick'
IGC_geo = args.IGC_geo
sim_num = args.sim_num
alignment_file = './' + '_'.join(paralog) + '/IGCgeo_' + str(
IGC_geo) + '/sim_' + str(sim_num) + '/' + '_'.join(
paralog) + '_MG94_geo_' + str(IGC_geo) + '_Sim_' + str(
sim_num) + '.fasta'
save_name = './SimulationSave/' + '_'.join(paralog) + '/IGCgeo_' + str(
IGC_geo) + '/' + '_'.join(paralog) + '_MG94_geo_' + str(
IGC_geo) + '_Sim_' + str(sim_num) + '_save.txt'
summary_name = './SimulationSummary/' + '_'.join(
paralog) + '/IGCgeo_' + str(IGC_geo) + '/' + '_'.join(
paralog) + '_MG94_geo_' + str(IGC_geo) + '_Sim_' + str(
sim_num) + '_summary.txt'
# generate folder if not exist
if not os.path.isdir('./SimulationSave/' + '_'.join(paralog) + '/'):
os.mkdir('./SimulationSave/' + '_'.join(paralog) + '/')
if not os.path.isdir('./SimulationSave/' + '_'.join(paralog) + '/IGCgeo_' +
str(IGC_geo) + '/'):
os.mkdir('./SimulationSave/' + '_'.join(paralog) + '/IGCgeo_' +
str(IGC_geo) + '/')
if not os.path.isdir('./SimulationSummary/' + '_'.join(paralog) + '/'):
os.mkdir('./SimulationSummary/' + '_'.join(paralog) + '/')
if not os.path.isdir('./SimulationSummary/' + '_'.join(paralog) +
'/IGCgeo_' + str(IGC_geo) + '/'):
os.mkdir('./SimulationSummary/' + '_'.join(paralog) + '/IGCgeo_' +
str(IGC_geo) + '/')
test = ReCodonGeneconv(newicktree,
alignment_file,
paralog,
Model='MG94',
Force=None,
clock=False,
save_name=save_name)
test.get_mle(False, True, 0, 'BFGS')
test.get_individual_summary(summary_path='./SimulationSummary/' +
'_'.join(paralog) + '/',
file_name=summary_name)
def main(args):
paralog = [args.paralog1, args.paralog2]
Force = None
clock = False
alignment_file = '../IdenticalParalogAlignment/' + '_'.join(
paralog) + '/' + '_'.join(paralog) + '_IdenticalParalog_input.fasta'
newicktree = './YeastTree.newick'
if args.force:
if model == 'MG94':
Force = {5: 0.0}
elif model == 'HKY':
Force = {4: 0.0}
else:
Force = None
test = ReCodonGeneconv(newicktree,
alignment_file,
paralog,
Model=args.model,
Force=Force,
clock=args.clock)
test.get_mle(True, True, 0, 'BFGS')
test.get_individual_summary(summary_path='./Summary/')
