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): 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): 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/')