def testLengthenEdge(self):
tree = create_tree_from_id2par(_bogus_id2par, ['hp', 'g', 'h'])
self.assertEqual(tree.find_node('hp')._id, 'hp')
li = tree.leaf_ids
li.sort()
self.assertEqual(li, ['g', 'h'])
tree.do_full_check_of_invariants(self, id2par=_bogus_id2par)
def testLengthenEdge(self):
tree = create_tree_from_id2par(_bogus_id2par, ['hp', 'g', 'h'])
self.assertEqual(tree.find_node('hp')._id, 'hp')
li = tree.leaf_ids
li.sort()
self.assertEqual(li, ['g', 'h'])
tree.do_full_check_of_invariants(self, id2par=_bogus_id2par)
def create_pruned_and_taxonomy_for_tip_ott_ids(tree_proxy, ott):
'''returns a pair of trees:
the first is that is a pruned version of tree_proxy created by pruning
any leaf that has no ott_id and every internal that does not have
any descendant with an ott_id. Nodes of out-degree 1 are suppressed
as part of the TreeWithPathsInEdges-style.
the second is the OTT induced tree for these ott_ids
'''
# create and id2par that has ott IDs only at the tips (we are
# ignoring mappings at internal nodes.
# OTT IDs are integers, and the nodeIDs are strings - so we should not get clashes.
#TODO consider prefix scheme
ott_ids = []
ottId2OtuPar = {}
for node in tree_proxy:
if node.is_leaf:
ott_id = node.ott_id
if ott_id is not None:
ott_ids.append(ott_id)
assert isinstance(ott_id, int)
parent_id = node.parent._id
ottId2OtuPar[ott_id] = parent_id
else:
assert is_str_type(node._id)
edge = node.edge
if edge is not None:
parent_id = node.parent._id
ottId2OtuPar[node._id] = parent_id
else:
ottId2OtuPar[node._id] = None
pruned_phylo = create_tree_from_id2par(ottId2OtuPar, ott_ids)
taxo_tree = ott.induced_tree(ott_ids)
return pruned_phylo, taxo_tree
def create_pruned_and_taxonomy_for_tip_ott_ids(tree_proxy, ott):
'''returns a pair of trees:
the first is that is a pruned version of tree_proxy created by pruning
any leaf that has no ott_id and every internal that does not have
any descendant with an ott_id. Nodes of out-degree 1 are suppressed
as part of the TreeWithPathsInEdges-style.
the second is the OTT induced tree for these ott_ids
'''
# create and id2par that has ott IDs only at the tips (we are
# ignoring mappings at internal nodes.
# OTT IDs are integers, and the nodeIDs are strings - so we should not get clashes.
#TODO consider prefix scheme
ott_ids = []
ottId2OtuPar = {}
for node in tree_proxy:
if node.is_leaf:
ott_id = node.ott_id
if ott_id is not None:
ott_ids.append(ott_id)
assert isinstance(ott_id, int)
parent_id = node.parent._id
ottId2OtuPar[ott_id] = parent_id
else:
assert is_str_type(node._id)
edge = node.edge
if edge is not None:
parent_id = node.parent._id
ottId2OtuPar[node._id] = parent_id
else:
ottId2OtuPar[node._id] = None
pruned_phylo = create_tree_from_id2par(ottId2OtuPar, ott_ids)
taxo_tree = ott.induced_tree(ott_ids)
return pruned_phylo, taxo_tree
def testCherry(self):
tree = create_tree_from_id2par(_bogus_id2par, ['h', 'p'])
self.assertTrue(tree._root._id == 'hp')
self.assertEqual(len(tree.leaves), 2)
i = tree.postorder_node_iter()
self.assertTrue(next(i)._id in ['h', 'p'])
self.assertTrue(next(i)._id in ['h', 'p'])
self.assertEqual(next(i)._id, 'hp')
self.assertRaises(StopIteration, next, i)
self.assertRaises(ValueError, create_tree_from_id2par, _bogus_id2par, ['h', 'bogus_tip'])
tree.do_full_check_of_invariants(self, id2par=_bogus_id2par)
def testCherry(self):
tree = create_tree_from_id2par(_bogus_id2par, ['h', 'p'])
self.assertTrue(tree._root._id == 'hp')
self.assertEqual(len(tree.leaves), 2)
i = tree.postorder_node_iter()
self.assertTrue(next(i)._id in ['h', 'p'])
self.assertTrue(next(i)._id in ['h', 'p'])
self.assertEqual(next(i)._id, 'hp')
self.assertRaises(StopIteration, next, i)
self.assertRaises(ValueError, create_tree_from_id2par, _bogus_id2par,
['h', 'bogus_tip'])
tree.do_full_check_of_invariants(self, id2par=_bogus_id2par)
def testFullExample(self):
tips = ['h', 'p', 'g', 'Po', 'Hy', 'Sy', 'Ho', 'No']
tree = create_tree_from_id2par(_bogus_id2par, tips)
tree.do_full_check_of_invariants(self, id2par=_bogus_id2par)
def testEmpty(self):
# not sure whether we should return an empty tree, None, or raise an exception...
self.assertEqual(None, create_tree_from_id2par(_bogus_id2par, []))
def testSingleton(self):
tree = create_tree_from_id2par(_bogus_id2par, ['h'])
self.assertEqual(tree.find_node('h')._id, 'h')
tree.do_full_check_of_invariants(self, id2par=_bogus_id2par)
def induced_tree(self, ott_id_list, create_monotypic_nodes=False):
# self._debug_anc_spikes(ott_id_list)
return create_tree_from_id2par(
self.ott_id2par_ott_id,
ott_id_list,
create_monotypic_nodes=create_monotypic_nodes)
def testFullExample(self):
tips = ['h', 'p', 'g', 'Po', 'Hy', 'Sy', 'Ho', 'No']
tree = create_tree_from_id2par(_bogus_id2par, tips)
tree.do_full_check_of_invariants(self, id2par=_bogus_id2par)
def testEmpty(self):
# not sure whether we should return an empty tree, None, or raise an exception...
self.assertEqual(None, create_tree_from_id2par(_bogus_id2par, []))
def testSingleton(self):
tree = create_tree_from_id2par(_bogus_id2par, ['h'])
self.assertEqual(tree.find_node('h')._id, 'h')
tree.do_full_check_of_invariants(self, id2par=_bogus_id2par)
def induced_tree(self, ott_id_list):
return create_tree_from_id2par(self.ott_id2par_ott_id, ott_id_list)
def induced_tree(self, ott_id_list):
return create_tree_from_id2par(self.ott_id2par_ott_id, ott_id_list)
def induced_tree(self, ott_id_list, create_monotypic_nodes=False):
# self._debug_anc_spikes(ott_id_list)
return create_tree_from_id2par(self.ott_id2par_ott_id, ott_id_list,
create_monotypic_nodes=create_monotypic_nodes)
