def test_changeFromParent(self):
"""TreeNode changeFromParent should record change from parent"""
t = DndParser('(a,(c,b)x,d)')
t.mapAttr({'a':5, 'c':3, 'b':7, 'x':2, 'd':1})
self.assertEqual(t[1][0].changeFromParent('Data'), 1)
self.assertEqual(t[1][1].changeFromParent('Data'), 5)
f = lambda x: x.Data * 2
self.assertEqual(t[1][0].changeFromParent(f), 2)
self.assertEqual(t[1][1].changeFromParent(f), 10)
def test_removeDeleted(self):
"""removeDeleted should remove all nodes where is_deleted tests true."""
tree = DndParser('((a:3,(b:2,(c:1,d:1):1):1):2,(e:3,f:3):2);',
constructor=TreeNode)
result_not_deleted = deepcopy(tree)
tree.removeDeleted(lambda x: x.Data in [])
self.assertEqual(str(tree),str(result_not_deleted))
deleted = Set(['b','d','e','f'])
result_tree = DndParser('((a:3,((c:1):1):1):2);',constructor=TreeNode)
is_deleted = lambda x: x.Data in deleted
tree.removeDeleted(is_deleted)
self.assertEqual(str(tree),str(result_tree))
def test_nodedata(self):
"""DndParser should assign Data to internal nodes correctly"""
t = DndParser(nodedata)
self.assertEqual(len(t), 2)
self.assertEqual(len(t[0]), 0) # first child is terminal
self.assertEqual(len(t[1]), 2) # second child has two children
self.assertEqual(str(t), "(abc:3.0,(def:4.0,ghi:5.0)jkl:6.0)")
info_dict = {}
for node in t.traverse():
info_dict[node.Data] = node.BranchLength
self.assertEqual(info_dict["abc"], 3.0)
self.assertEqual(info_dict["def"], 4.0)
self.assertEqual(info_dict["ghi"], 5.0)
self.assertEqual(info_dict["jkl"], 6.0)
def test_mapAttr(self):
"""Tree mapattr should correctly change the attributes in-place"""
t = DndParser('(a,(c,b)x,d)')
t.mapAttr({'a':'aa','b':'bb','c':'cc','x':'xx'}) # d left out
self.assertEqual(str(t), '(aa,(cc,bb)xx,d)')
t = DndParser('(a,(c,b)x,d)')
f = lambda x: x in list('abcx') and x*3 or x
t.mapAttr(f) # d left out
self.assertEqual(str(t), '(aaa,(ccc,bbb)xxx,d)')
#check that it works if you set a different attribute than you read
t = DndParser('(a,(c,b)x,d)')
t.mapAttr(f, new_attr='xxx')
for n in t.traverse(self_before=True, self_after=False):
if n in list('abcx'):
self.assertEqual(n.xxx, n.Data*3)
else:
self.assertEqual(n.xxx, n.Data)
def test_attrTable(self):
""""TreeNode attrTable should return correct table of attributes"""
t = DndParser('(a,(c,b)x,d)')
f1 = lambda x: x in list('abcx') and x*2 or x
f2 = lambda x: x in list('abcx') and x*3 or x
f3 = lambda x: x in list('abcx') and x*4 or x
t.mapAttr(f1, new_attr='xx')
t.mapAttr(f2, new_attr='xxx')
t.mapAttr(f3, new_attr='xxxx')
table = t.attrTable(['xx','xxxx'])
self.assertEqual(table, [[None, None], ['aa','aaaa'],['xx','xxxx'],\
['cc','cccc'],['bb','bbbb'],['d','d']])
def GSC_weightnode_dependent(tree):
"""GSC method depending on the NodeWeight object implemented by Micah Hamady
"""
weight_node = DndParser(str(tree),constructor=WeightNode)
weight_node.setWeights()
return weight_node.leafWeights()
"""
mean_name = prop_name+'WeightedMean'
stdev_name = prop_name+'WeightedStdev'
for n in self.traverse(self_before=False, self_after=True):
if not n.Children:
setattr(n, mean_name, f(n))
setattr(n, stdev_name, 0)
else:
num = 0
den = 0
branchlengths = [max(c.BranchLength, branch_delta) \
for c in n.Children]
child_vals = [getattr(c, mean_name) for c in n.Children]
num = sum([(1.0*i)/j for i, j in zip(child_vals, branchlengths)])
den = sum([1.0/j for j in branchlengths])
result = num/den
setattr(n, mean_name, result)
std = sqrt(sum([(c-result)**2 for c in child_vals])\
/len(child_vals))
setattr(n, stdev_name, std)
if __name__ == '__main__':
from old_cogent.parse.tree import DndParser
s = '((a:7.9,((b:0.1,c:0.1):0.1,d:0.2):7.7):0.1,e:8.0)'
t = DndParser(s)
print t
t.scaleBranchLengths(8, ultrametric=True)
print t
def test_prune(self):
"""prune should recconstruct correct topology of tree."""
tree = DndParser('((a:3,((c:1):1):1):2);',constructor=TreeNode)
tree.prune()
result_tree = DndParser('((a:3,c:1));',constructor=TreeNode)
self.assertEqual(str(tree),str(result_tree))
