def RootAllTrees():
import tree
speciesIDs = util.FirstWordExtractor("SpeciesIDs.txt").GetIDToNameDict()
species_tree_rooted = tree.Tree("SpeciesTree_ids_0_rooted_unresolved.txt")
GeneToSpecies = GeneToSpecies_dash
for fn in glob.glob("Trees_ids/OG*txt"):
print("*** " + fn + " ***")
t = tree.Tree(fn)
root = GetRoot(t, species_tree_rooted, GeneToSpecies)
if root == None:
print("Fail: " + fn)
else:
if root != t:
t.set_outgroup(root)
for n in t:
n.name = speciesIDs[n.name.split("_")[0]]
t.write(outfile="Trees_ids_rooted/" + os.path.split(fn)[1])
util.Success()
parser.add_argument("trees_dir")
parser.add_argument("rooted_species_tree")
# parser.add_argument("-p", "--prune", action='store_true')
parser.add_argument("-s", "--separator", choices=("dot", "dash", "second_dash", "3rd_dash", "hyphen"), help="Separator been species name and gene name in gene tree taxa")
args = parser.parse_args()
output_dir = os.path.split(args.trees_dir)[0]
qSingleTree = False
try:
tree_lib.Tree(args.trees_dir)
qSingleTree = True
print("Analysing single tree")
except:
try:
tree = tree_lib.Tree(args.trees_dir)
qSingleTree = True
except:
pass
if not os.path.exists(output_dir):
os.mkdir(output_dir)
GeneToSpecies = GetGeneToSpeciesMap(args)
output_dir = output_dir + "/../Orthologues_M3/"
print(output_dir)
if not os.path.exists(output_dir):
os.mkdir(output_dir)
# GetOrthologuesStandalone_Parallel(args.trees_dir, args.rooted_species_tree, GeneToSpecies, output_dir, qSingleTree)
GetOrthologuesStandalone_Serial(args.trees_dir, args.rooted_species_tree, GeneToSpecies, output_dir, qSingleTree)
# RootTreeStandalone_Serial(args.trees_dir, args.rooted_species_tree, GeneToSpecies, output_dir, qSingleTree)
util.Success()
