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 )
'''
