def test_make_distance_based_exclusion_fn(self):
"""make_distance_based_exclusion_fn should return a working function"""
exclude_similar_strains = make_distance_based_exclusion_fn(0.03)
# Test that new function is documented
exp_doc = "Exclude neighbors of tip within 0.030000 branch length units"
self.assertEqual(exp_doc, exclude_similar_strains.__doc__)
# Test that the function works
test_tree = self.SimpleTree.deepcopy()
# print test_tree.getNewick(with_distances=True)
tip = test_tree.getNodeMatchingName("C")
obs = exclude_similar_strains(tip, test_tree).getNewick(with_distances=True)
exp = "(A:0.02,B:0.01)root;"
self.assertEqual(obs, exp)
# Test on a tree where a single node will remain
test_tree = DndParser("((A:0.02,B:0.01)E:0.05,(C:0.06,D:0.01)F:0.05)root;")
# print test_tree.getNewick(with_distances=True)
tip = test_tree.getNodeMatchingName("D")
obs = exclude_similar_strains(tip, test_tree).getNewick(with_distances=True)
exp = "((A:0.02,B:0.01)E:0.05,C:0.11)root;"
self.assertEqual(obs, exp)
# Test that we raise if distance is too large
test_tree = self.SimpleTree.deepcopy()
test_fn = make_distance_based_exclusion_fn(300.0)
tip = test_tree.getNodeMatchingName("C")
self.assertRaises(ValueError, test_fn, tip, test_tree)
def test_yield_test_trees(self):
"""yield_test_trees should yield modified test trees"""
start_tree = self.SimpleTree.deepcopy()
# First, test with simple tree and exclude_tip
# (not a typical use, but easy to predict
# and still important to test)
test_fn = exclude_tip
obs = [o for o in yield_test_trees(start_tree, test_fn)]
test_tips = [tip for tip, tree in obs]
test_trees = [tree for tip, tree in obs]
#print test_tips
#print test_trees
#Test that each tree excludes the correct tip
for i, exp_tip in enumerate(start_tree.tips()):
#print exp_tip
node_names = [obs_tip.Name for obs_tip in test_trees[i].tips()]
#print node_names
self.assertTrue(exp_tip.Name not in node_names)
#Test that the topology is correct for an example tree
self.assertTrue(test_trees[1].getNewick(with_distances=True) in\
["((C:0.01,D:0.01)F:0.05,A:0.07)root;","(A:0.07,(C:0.01,D:0.01)F:0.05)root;"])
#Second, let's test a more realistic test function
test_fn = make_distance_based_exclusion_fn(0.03)
obs = [o for o in yield_test_trees(start_tree, test_fn)]
test_tips = [tip for tip, tree in obs]
test_trees = [tree for tip, tree in obs]
#Test that each tree excludes the tip of interest
#NOTE: this behavior changed some time ago
#We want to exclude the test tip.
for i, exp_tip in enumerate(start_tree.tips()):
#print exp_tip
node_names = [obs_tip.Name for obs_tip in test_trees[i].tips()]
#print node_names
self.assertFalse(exp_tip.Name in node_names)
#Test that the topology is correct for all tips
#Tip 'A'
self.assertEqual(test_trees[0].getNewick(with_distances=True),\
"(C:0.01,D:0.01)root;")
#Tip 'B'
self.assertEqual(test_trees[1].getNewick(with_distances=True),\
"(C:0.01,D:0.01)root;")
#Tip 'C'
self.assertEqual(test_trees[2].getNewick(with_distances=True),\
"(A:0.02,B:0.01)root;")
#Tip 'D'
self.assertEqual(test_trees[3].getNewick(with_distances=True),\
"(A:0.02,B:0.01)root;")
def test_yield_test_trees(self):
"""yield_test_trees should yield modified test trees"""
start_tree = self.SimpleTree.deepcopy()
# First, test with simple tree and exclude_tip
# (not a typical use, but easy to predict
# and still important to test)
test_fn = exclude_tip
obs = [o for o in yield_test_trees(start_tree, test_fn)]
test_tips = [tip for tip, tree in obs]
test_trees = [tree for tip, tree in obs]
# print test_tips
# print test_trees
# Test that each tree excludes the correct tip
for i, exp_tip in enumerate(start_tree.tips()):
# print exp_tip
node_names = [obs_tip.Name for obs_tip in test_trees[i].tips()]
# print node_names
self.assertTrue(exp_tip.Name not in node_names)
# Test that the topology is correct for an example tree
self.assertTrue(
test_trees[1].getNewick(with_distances=True)
in ["((C:0.01,D:0.01)F:0.05,A:0.07)root;", "(A:0.07,(C:0.01,D:0.01)F:0.05)root;"]
)
# Second, let's test a more realistic test function
test_fn = make_distance_based_exclusion_fn(0.03)
obs = [o for o in yield_test_trees(start_tree, test_fn)]
test_tips = [tip for tip, tree in obs]
test_trees = [tree for tip, tree in obs]
# Test that each tree excludes the tip of interest
# NOTE: this behavior changed some time ago
# We want to exclude the test tip.
for i, exp_tip in enumerate(start_tree.tips()):
# print exp_tip
node_names = [obs_tip.Name for obs_tip in test_trees[i].tips()]
# print node_names
self.assertFalse(exp_tip.Name in node_names)
# Test that the topology is correct for all tips
# Tip 'A'
self.assertEqual(test_trees[0].getNewick(with_distances=True), "(C:0.01,D:0.01)root;")
# Tip 'B'
self.assertEqual(test_trees[1].getNewick(with_distances=True), "(C:0.01,D:0.01)root;")
# Tip 'C'
self.assertEqual(test_trees[2].getNewick(with_distances=True), "(A:0.02,B:0.01)root;")
# Tip 'D'
self.assertEqual(test_trees[3].getNewick(with_distances=True), "(A:0.02,B:0.01)root;")
def test_make_distance_based_exclusion_fn(self):
"""make_distance_based_exclusion_fn should return a working function"""
exclude_similar_strains =\
make_distance_based_exclusion_fn(0.03)
#Test that new function is documented
exp_doc = 'Exclude neighbors of tip within 0.030000 branch length units'
self.assertEqual(exp_doc, exclude_similar_strains.__doc__)
#Test that the function works
test_tree = self.SimpleTree.deepcopy()
#print test_tree.getNewick(with_distances=True)
tip = test_tree.getNodeMatchingName('C')
obs = exclude_similar_strains(tip,
test_tree).getNewick(with_distances=True)
exp = "(A:0.02,B:0.01)root;"
self.assertEqual(obs, exp)
#Test on a tree where a single node will remain
test_tree = \
DndParser("((A:0.02,B:0.01)E:0.05,(C:0.06,D:0.01)F:0.05)root;")
#print test_tree.getNewick(with_distances=True)
tip = test_tree.getNodeMatchingName('D')
obs = exclude_similar_strains(tip,
test_tree).getNewick(with_distances=True)
exp = "((A:0.02,B:0.01)E:0.05,C:0.11)root;"
self.assertEqual(obs, exp)
#Test that we raise if distance is too large
test_tree = self.SimpleTree.deepcopy()
test_fn = make_distance_based_exclusion_fn(300.0)
tip = test_tree.getNodeMatchingName('C')
self.assertRaises(ValueError, test_fn, tip, test_tree)
