def test_load_tree(self):
# test to load a given tree-file
tree = LoadTree(test_data('phylogeny.tre'))
taxa = sorted(["Beijing", "Changsha", "Chengdu", "Fuzhou", "Guangzhou",
"Guiyang", "Haerbin", "Haikou", "Hangzhou", "Hefei",
"Huhehaote", "Jian\u2019ou", "Jinan", "Kunming",
"Lanzhou",
"Meixian", "Nanchang", "Nanjing", "Nanning", "Pingyao",
"Qingdao", "Shanghai", "Shantou", "Shexian", "Suzhou",
"Taibei", "Taiyuan", "Taoyuan", "Tianjin", "Tunxi",
"Wenzhou", "Wuhan", "Wulumuqi", "Xi\u2019an", "Xiamen",
"Xianggang", "Xiangtan", "Xining", "Yinchuan",
"Zhengzhou"])
for a, b in zip(sorted(tree.taxa), taxa):
assert a == b
tree = LoadTree("((((((((Taiyuan,Pingyao,Huhehaote),"
"((((Xi’an,Xining,Zhengzhou),(Lanzhou,Yinchuan,"
"Wulumuqi)),"
"(((Tianjin,Jinan),Qingdao),Beijing,Haerbin)),"
"(((Guiyang,Kunming),Chengdu,Wuhan),(Nanjing,Hefei)))),"
"(Xiangtan,Changsha)),Nanchang),(Shexian,Tunxi)),"
"((Shanghai,Suzhou,Hangzhou),Wenzhou)),"
"(((Xianggang,Guangzhou),Nanning),(Meixian,Taoyuan))),"
"((((Xiamen,Taibei),Shantou,Haikou),Fuzhou),Jian’ou));")
for a, b in zip(sorted(tree.taxa), taxa):
assert a == b
def __init__(self, tree, **keywords):
# this is an absolutely nasty hack, but it helps us to maintain
# lingpy-specific aspects of cogent's trees and allows us to include
# them in our documentation
if type(tree) == str:
if tree[-4:] not in ['.nwk', '.txt']:
tmp = LoadTree(treestring=tree)
else:
tmp = LoadTree(tree)
else:
if type(tree) == list:
tmp = LoadTree(treestring=random_tree(tree, **keywords))
else:
tmp = LoadTree(tree)
for key, val in tmp.__dict__.items():
self.__dict__[key] = val
self._edge_len = len(self.getNodeNames()) - 1
def __init__(self, tree, **keywords):
# this is an absolutely nasty hack, but it helps us to maintain
# lingpy-specific aspects of cogent's trees and allows us to include
# them in our documentation
if type(tree) == str:
if not os.path.isfile(tree):
tmp = LoadTree(treestring=tree)
else:
tmp = LoadTree(tree)
else:
if type(tree) == list:
tmp = LoadTree(treestring=random_tree(tree, **keywords))
else: # pragma: no cover
# last ditch attempt to try load
tmp = LoadTree(tree)
for key, val in tmp.__dict__.items():
self.__dict__[key] = val
self._edge_len = len(self.getNodeNames()) - 1
def test_more_trees(self):
tree = LoadTree('((a:1,b:1):2,(c:3,d:4):5);')
tree2 = LoadTree('((a,b),(c,d));')
assert tree.sameShape(tree)
tree.tipToTipDistances()
tree.getMaxTipTipDistance()
tree.maxTipTipDistance()
tree.getSubTree(['a','b','c'])
assert tree.compareName(tree2) == 0
assert tree.compareName(tree) == 0
assert tree.compareName('(a,b),(c,d));') != 0
tree.descendantArray()
tree.nameUnnamedNodes()
tree.makeTreeArray()
tree.getNewickRecursive(with_distances=True, semicolon=False,
escape_name=False)
assert 'a' in tree.getNodesDict()
assert 'b' in tree.taxa
assert tree.getDistances()['a', 'b'] == 2
assert tree.getMaxTipTipDistance()[0] == 12
assert tree.maxTipTipDistance()[0] == 12
ntree = tree.copyRecursive()
ntree2 = tree2.copy()
assert ntree.sameShape(ntree2)
assert 'a' in tree.getNodeNames()
assert_raises(TreeParseError, LoadTree, '(a,b;');
assert_raises(TreeParseError, LoadTree, treestring="(a,b'");
assert_raises(TreeParseError, LoadTree, treestring="(a,'b'");
assert_raises(TreeParseError, LoadTree, treestring="(a,'b'\n");
assert_raises(TreeParseError, LoadTree, treestring="(a,'b-c'");
assert_raises(TreeParseError, LoadTree, "(a,b),('c_d',e);")
new_tree = LoadTree("((a,b),('',e));")
new_tree.nameUnnamedNodes()
def test_load_tree(test_data):
# test to load a given tree-file
tree = LoadTree(str(test_data / 'phylogeny.tre'))
assert tree.compareByPartitions(tree) == 0
taxa = sorted([
"Beijing", "Changsha", "Chengdu", "Fuzhou", "Guangzhou", "Guiyang",
"Haerbin", "Haikou", "Hangzhou", "Hefei", "Huhehaote", "Jian\u2019ou",
"Jinan", "Kunming", "Lanzhou", "Meixian", "Nanchang", "Nanjing",
"Nanning", "Pingyao", "Qingdao", "Shanghai", "Shantou", "Shexian",
"Suzhou", "Taibei", "Taiyuan", "Taoyuan", "Tianjin", "Tunxi",
"Wenzhou", "Wuhan", "Wulumuqi", "Xi\u2019an", "Xiamen", "Xianggang",
"Xiangtan", "Xining", "Yinchuan", "Zhengzhou"
])
assert len(tree.getConnectingEdges('Beijing', 'Xiangtan')) == 8
for a, b in zip(sorted(tree.taxa), taxa):
assert a == b
tree.removeNode('Beijing')
tree.prune()
tree = LoadTree(tip_names=['Beijing', 'Changsha'])
assert len(tree.taxa) == 2
tree = LoadTree("((((((((Taiyuan,Pingyao,Huhehaote),"
"((((Xi’an,Xining,Zhengzhou),(Lanzhou,Yinchuan,"
"Wulumuqi)),"
"(((Tianjin,Jinan),Qingdao),Beijing,Haerbin)),"
"(((Guiyang,Kunming),Chengdu,Wuhan),(Nanjing,Hefei)))),"
"(Xiangtan,Changsha)),Nanchang),(Shexian,Tunxi)),"
"((Shanghai,Suzhou,Hangzhou),Wenzhou)),"
"(((Xianggang,Guangzhou),Nanning),(Meixian,Taoyuan))),"
"((((Xiamen,Taibei),Shantou,Haikou),Fuzhou),Jian’ou));")
for a, b in zip(sorted(tree.taxa), taxa):
assert a == b