class BigTreeSingleTests(TestTree):
"""using the big-tree for single-tree tests"""
def setUp(self):
self.name = 'big tree - '
self.otu_names = [
'Horse', 'TombBat', 'Rhino', 'Pig', 'AsianElep', 'SpermWhal',
'Cat', 'Gorilla', 'Orangutan', 'bandicoot', 'Hedgehog', 'Sloth',
'HairyArma', 'Manatee', 'GoldenMol', 'Pangolin'
]
self.otu_names.sort()
self.newick = '((((((((FlyingFox,DogFaced),((FreeTaile,LittleBro),(TombBat,RoundEare))),(FalseVamp,LeafNose)),(((Horse,Rhino),(Pangolin,(Cat,Dog))),(Llama,(Pig,(Cow,(Hippo,(SpermWhal,HumpbackW))))))),(Mole,Hedgehog)),(TreeShrew,(FlyingLem,((Jackrabbit,(FlyingSqu,(OldWorld,(Mouse,Rat)))),(Galago,(HowlerMon,(Rhesus,(Orangutan,(Gorilla,(Human,Chimpanzee)))))))))),(((NineBande,HairyArma),(Anteater,Sloth)),(((Dugong,Manatee),((AfricanEl,AsianElep),(RockHyrax,TreeHyrax))),(Aardvark,((GoldenMol,(Madagascar,Tenrec)),(LesserEle,GiantElep)))))),(caenolest,(phascogale,(wombat,bandicoot))));'
self.newick_reduced = '(((((TombBat,(((Horse,Rhino),(Pangolin,Cat)),(Pig,SpermWhal))),Hedgehog),(Orangutan,Gorilla)),((HairyArma,Sloth),((Manatee,AsianElep),GoldenMol))),bandicoot);'
self.tree = LoadTree(treestring=self.newick)
def test_getEdgeNames(self):
"""testing (well, exercising at least), getedgenames"""
# Fell over on small tree because "stem descended from root
# joiner was a tip"
a, b = self.otu_names[:2]
clade = self.tree.getEdgeNames(a, b, True, False)
def test_getTipNames(self):
"""testing (well, exercising at least), getTipNames"""
a, b = self.otu_names[:2]
tips = self.tree.getTipNames()
self.assertEqual(len(tips), 55)
def test_making_from_list(self):
tipnames_with_spaces = ['a_b', 'a b', "T'lk"]
tipnames_with_spaces.sort()
t = LoadTree(tip_names=tipnames_with_spaces)
result = t.getTipNames()
result.sort()
assert result == tipnames_with_spaces
class BigTreeSingleTests(TestTree):
"""using the big-tree for single-tree tests"""
def setUp(self):
self.name = 'big tree - '
self.otu_names = ['Horse', 'TombBat', 'Rhino', 'Pig', 'AsianElep',
'SpermWhal', 'Cat', 'Gorilla', 'Orangutan',
'bandicoot', 'Hedgehog', 'Sloth', 'HairyArma',
'Manatee', 'GoldenMol', 'Pangolin']
self.otu_names.sort()
self.newick = '((((((((FlyingFox,DogFaced),((FreeTaile,LittleBro),(TombBat,RoundEare))),(FalseVamp,LeafNose)),(((Horse,Rhino),(Pangolin,(Cat,Dog))),(Llama,(Pig,(Cow,(Hippo,(SpermWhal,HumpbackW))))))),(Mole,Hedgehog)),(TreeShrew,(FlyingLem,((Jackrabbit,(FlyingSqu,(OldWorld,(Mouse,Rat)))),(Galago,(HowlerMon,(Rhesus,(Orangutan,(Gorilla,(Human,Chimpanzee)))))))))),(((NineBande,HairyArma),(Anteater,Sloth)),(((Dugong,Manatee),((AfricanEl,AsianElep),(RockHyrax,TreeHyrax))),(Aardvark,((GoldenMol,(Madagascar,Tenrec)),(LesserEle,GiantElep)))))),(caenolest,(phascogale,(wombat,bandicoot))));'
self.newick_reduced = '(((((TombBat,(((Horse,Rhino),(Pangolin,Cat)),(Pig,SpermWhal))),Hedgehog),(Orangutan,Gorilla)),((HairyArma,Sloth),((Manatee,AsianElep),GoldenMol))),bandicoot);'
self.tree = LoadTree(treestring = self.newick)
def test_getEdgeNames(self):
"""testing (well, exercising at least), getedgenames"""
# Fell over on small tree because "stem descended from root
# joiner was a tip"
a,b = self.otu_names[:2]
clade = self.tree.getEdgeNames(a, b, True, False)
def test_getTipNames(self):
"""testing (well, exercising at least), getTipNames"""
a,b = self.otu_names[:2]
tips = self.tree.getTipNames()
self.assertEqual(len(tips), 55)
def test_making_from_list(self):
tipnames_with_spaces = ['a_b','a b',"T'lk"]
tipnames_with_spaces.sort()
t = LoadTree(tip_names=tipnames_with_spaces)
result = t.getTipNames()
result.sort()
assert result == tipnames_with_spaces
def load_de_numericized_newick_tree(tree_in,before="'",after="'",root=False):
from cogent.core.tree import PhyloNode
from cogent import LoadTree
import os.path
if os.path.isfile(tree_in):
tree = LoadTree(tree_in)
else:
tree = LoadTree(treestring=tree_in)
terminals = tree.getTipNames()
rename_dict = {}
for tip in terminals:
rename_dict[tip] = before + str(tip) + after
tree.reassignNames(rename_dict)
if root:
tree = tree.rootAtMidpoint()
treestring = tree.getNewick(with_distances=True)
return treestring
