def test_best_allow_root(self):
def score_f(global_seq_scores, local_seq_scores, node):
return len(local_seq_scores)
exp = {'query1': {'node': self.tree.find('root'), 'score': 2},
'query2': {'node': self.tree.find('h'), 'score': 2}}
def score_f(global_seq_scores, local_seq_scores, node):
return len(local_seq_scores)
obs = best(score(propagate(decorate(self.tree, self.mock_hits,
threshold=11.0)),
score_f))
self.assertEqual(obs, exp)
def test_propagate(self):
exp = self.tree.copy()
exp.find('a').hits = {'query1': [95.6]}
exp.find('b').hits = {}
exp.find('c').hits = {'query1': [95.6]}
exp.find('d').hits = {}
exp.find('e').hits = {'query1': [95.6]}
exp.find('f').hits = {'query1': [15.7], 'query2': [90.6]}
exp.find('g').hits = {'query2': [12.7]}
exp.find('h').hits = {'query1': [15.7], 'query2': [90.6, 12.7]}
exp.hits = {'query1': [95.6, 15.7], 'query2': [90.6, 12.7]}
obs = propagate(decorate(self.tree, self.mock_hits, threshold=11.0))
for o, e in zip(obs.traverse(), exp.traverse()):
self.assertEqual(o.hits.keys(), e.hits.keys())
for o_key in o.hits:
npt.assert_equal(o.hits[o_key], e.hits[o_key])
def test_score(self):
def score_f(global_seq_scores, local_seq_scores, node):
return len(local_seq_scores)
exp = self.tree.copy()
exp.find('a').scores = {'query1': 1}
exp.find('b').scores = {}
exp.find('c').scores = {'query1': 1}
exp.find('d').scores = {}
exp.find('e').scores = {'query1': 1}
exp.find('f').scores = {'query1': 1, 'query2': 1}
exp.find('g').scores = {'query2': 1}
exp.find('h').scores = {'query1': 1, 'query2': 2}
exp.scores = {'query1': 2, 'query2': 2}
obs = propagate(decorate(self.tree, self.mock_hits, threshold=11.0))
obs = score(obs, score_f)
for o, e in zip(obs.traverse(), exp.traverse()):
self.assertEqual(o.scores, e.scores)
def test_best_no_root(self):
def score_f(global_seq_scores, local_seq_scores, node):
return len(local_seq_scores)
def battle_f(cur_node, existing_node, cur_score, existing_score):
if cur_node.is_root():
return False
if cur_score > existing_score:
return True
if cur_score == existing_score:
return cur_node.min_tip_dist < existing_node.min_tip_dist
return False
exp = {'query1': {'node': self.tree.find('a'), 'score': 1},
'query2': {'node': self.tree.find('h'), 'score': 2}}
obs = best(score(propagate(decorate(self.tree, self.mock_hits,
threshold=11.0)),
score_f),
battle_f=battle_f)
self.assertEqual(obs, exp)
def test_insert(self):
def battle_f(cur_node, existing_node, cur_score, existing_score):
if cur_node.is_root():
return False
if cur_score > existing_score:
return True
if cur_score == existing_score:
return cur_node.min_tip_dist < existing_node.min_tip_dist
return False
def score_f(global_seq_scores, local_seq_scores, node):
return len(local_seq_scores)
insert(best(score(propagate(decorate(self.tree, self.mock_hits,
threshold=11.0)),
score_f),
battle_f=battle_f),
threshold=2)
node = self.tree.find('query2')
self.assertTrue(node.parent is self.tree.find('h'))
with self.assertRaises(skbio.tree.MissingNodeError):
self.tree.find('query1')
def test_all_seq_scores(self):
exp = {'query1': [95.6, 10.7, 15.7], 'query2': [90.6, 12.7]}
obs = _all_seq_scores(propagate(decorate(self.tree, self.mock_hits)))
self.assertEqual(obs.keys(), exp.keys())
for k in obs:
npt.assert_equal(obs[k], exp[k])