from pylogeny.tree import tree # import tree class definition
t = tree("(10,((11,(4,(1,(3,2)))),(9,((5,6),(8,7)))));"
) # instantiate with this Newick string
#print t
topo = t.toTopology() # converts a tree to a rich object of branches and nodes
rearrList = topo.allSPR() # a list of rearrangement objects
for rearr in rearrList:
move = rearr.doMove(
) # perform the rearrangement and get a topology object
print move # prints the Newick string for this topology
#foo(move) # do something with this topology
def test_tree_initNoCheck(self):
t = tree(self.tree_.getNewick(), check=False)
self.assertTrue(type(t) == tree)
self.assertEqual(t.newick, self.tree_.getNewick())
def test_tree_init(self):
t = tree(self.tree_.getNewick(), check=True)
self.assertTrue(type(t) == tree)
# From Ishrat Jahan of UIU
from pylogeny.tree import tree # import tree class definition
t = tree(
"(GAL,(ORN,((MAC,MON),(((CHO,DAS),(ECH,(LOX,PRO))),(((TUP,((ORY,OCH),(SPE,(CAV,(DIP,(MUS,RAT)))))),((OTO,MIC),(TAR,(CAL,(NEW,(PON,(GOR,(PAN,HOM)))))))),((SOR,ERI),((MYO,PTE),(((FEL,CAN),(VIC,(SUS,(TUR,BOS)))),EQU))))))));"
) # instantiate with this Newick string
#print t
topo = t.toTopology() # converts a tree to a rich object of branches and nodes
rearrList = topo.allSPR() # a list of rearrangement objects
for rearr in rearrList:
move = rearr.doMove(
) # perform the rearrangement and get a topology object
print(move) # prints the Newick string for this topology
#foo(move) # do something with this topology
def test_tree_initNoCheck(self):
t = tree(self.tree_.getNewick(),check=False)
self.assertTrue(type(t) == tree)
self.assertEqual(t.newick,self.tree_.getNewick())
def test_tree_init(self):
t = tree(self.tree_.getNewick(),check=True)
self.assertTrue(type(t) == tree)