def setUp(self):
self.node0 = taxidTools.Node(taxid=0,
name="root",
rank="root",
parent=None)
self.node1 = taxidTools.Node(taxid=1,
name="node1",
rank="rank1",
parent=self.node0)
self.node2 = taxidTools.Node(taxid=2,
name="node2",
rank="rank1",
parent=self.node0)
self.node11 = taxidTools.Node(taxid=11,
name="node11",
rank="rank2",
parent=self.node1)
self.node12 = taxidTools.Node(taxid=12,
name="node12",
rank="rank2",
parent=self.node1)
self.node21 = taxidTools.Node(taxid=21,
name="node21",
rank="rank2",
parent=self.node2)
self.node22 = taxidTools.Node(taxid=22,
name="node22",
rank="rank2",
parent=self.node2)
self.node23 = taxidTools.Node(taxid=23,
name="node23",
rank="rank2",
parent=self.node2)
self.node121 = taxidTools.Node(taxid=121,
name="node121",
rank="rank3",
parent=self.node12)
self.node122 = taxidTools.Node(taxid=122,
name="node122",
rank="rank3",
parent=self.node12)
nodes = {
"0": self.node0,
"1": self.node1,
"2": self.node2,
"11": self.node11,
"12": self.node12,
"21": self.node21,
"22": self.node22,
"23": self.node23,
"121": self.node121,
"122": self.node122
}
self.txd = taxidTools.Taxonomy(nodes)
def setUp(self):
self.parent = taxidTools.Node(taxid=0,
name="root",
rank="root",
parent=None)
self.child = taxidTools.Node(taxid=1,
name="child",
rank="child",
parent=self.parent)
self.txd = taxidTools.Taxonomy({'0': self.parent, '1': self.child})
def test_consensus_dummynodes(self):
node0 = taxidTools.Node(0)
node1 = taxidTools.Node(1, parent=node0)
dummy1 = taxidTools.DummyNode(parent=node0)
node2 = taxidTools.Node(2, parent=node1)
node3 = taxidTools.Node(3, parent=dummy1)
node4 = taxidTools.Node(4, parent=dummy1)
tax = taxidTools.Taxonomy.from_list(
[node0, node1, dummy1, node2, node3, node4])
cons = tax.consensus(["2", "3", "4"], 0.51)
self.assertEqual(cons, node0)
def test_insert_nodes_recc(self):
node001 = taxidTools.Node('001',
name="node0011",
rank="rank3",
parent=self.node0)
node3 = taxidTools.Node('3',
name="node3",
rank="rank1",
parent=self.node0)
self.txd.addNode(node3)
new_nodes = _insert_nodes_recc(self.node0,
['rank3', 'rank2', 'rank1.5', 'rank1'])
self.assertEqual(len(new_nodes), 15)
def test_filter(self):
node001 = taxidTools.Node('001',
name="node0011",
rank="rank3",
parent=self.node0)
self.txd.addNode(node001)
self.txd.filterRanks(ranks=['rank3', 'rank1'])
self.assertEqual(len(self.txd), 8)
# test relinking
self.assertEqual(self.node121.parent, self.node1)
self.assertIsInstance(node001.parent, taxidTools.DummyNode)
def setUp(self):
self.parent = taxidTools.Node(taxid = 0, name = "root", rank = "root", parent = None)
self.rank1 = taxidTools.Node(taxid = 1, name = "node1", rank = "rank1", parent = self.parent)
self.rank2 = taxidTools.Node(taxid = 2, name = "node2", rank = "rank2", parent = self.rank1)
self.rank3 = taxidTools.Node(taxid = 3, name = "node3", rank = "rank3", parent = self.rank2)
def setUp(self):
self.node = taxidTools.Node(taxid=123456)
self.midnode = taxidTools.Node(taxid=2, parent=self.node)
self.lownode = taxidTools.Node(taxid=3, parent=self.midnode)
def test_parent(self):
parent1 = taxidTools.Node(taxid=789)
self.node.parent = parent1
self.assertEqual(self.node.parent.taxid, "789")