def makeBayestreeouts(tree, treehome): if not os.path.exists(treehome + "\\" + tree + "_bayes_treeout.txt"): os.chdir(treehome) tree_extract = BayesExtract(tree, treehome + "\\" + tree + ".nex", treehome, 1000) tree_extract.treeMatch() trees_file_name = treehome + tree + "_bayes_treeout.txt" shutil.copyfile(tree + "treeout.txt", trees_file_name) # Add the base tree in at line one: infile1 = open(trees_file_name,'r') infile2 = open(tree + ".txt",'r') outfile = open(treehome + "temptrees.txt",'w') outfile.write(infile2.readline()+"\n") infile2.close() for line in infile1: outfile.write(line) infile1.close() outfile.close() shutil.copyfile("temptrees.txt",trees_file_name) else: print("Skipping Mr Bayes treeout extraction - already done for " + tree)
print("Skipping Mr Bayes Driver generation - already done") # Run Mr. Bayes MCMC ''' if not os.path.exists(seq_dir + tree + "\\" + tree + ".nex" + ".mcmc"): os.chdir(seq_tree_dir) command = bayes_exe + " " + tree + "-command.nex" call(command.split()) else: print("Skipping Mr Bayes MCMC - already done") ''' # Create Bayes treeout if not os.path.exists(seq_dir + tree + "\\" + tree + "treeout.txt"): os.chdir(seq_tree_dir) tree_extract = BayesExtract(tree,seq_tree_dir + tree + ".nex", seq_tree_dir,1000) tree_extract.treeMatch() ''' # Run Raxml if needed with default GTR parameters rax_path = "c:/raxml" rax_ver = "raxmlHPC" raxml_dir = "/raxml" data_name = tree rax_treeout = tree + "treeout.txt" if not os.path.exists(raxml_dir): os.mkdir(raxml_dir) os.system('./' + rax_ver + ' -s ' + seq_dir + '/' + data_name + '/' + data_name + '.nex' + ' -n ' + data_name + ' -m GTRGAMMA -e 0.001 -f a -k -x 27362 -p 96618 -N 1000 -w ' + os.getcwd() + '/' + raxml_dir ) '''