def test_four(self):
text = ("(0,((((((((1,((2,3),4)),(5,6)),(((7,(8,9)),10),"
"((11,((((12,13),(14,15)),16),17)),((18,19),(20,21))))),"
"(22,23)),(((24,25),26),((27,28),(29,((30,31),((((32,33),"
"(34,(35,(36,37)))),(38,(39,((40,41),42)))),43)))))),44),45),46));")
enewick_graph = enewick_to_digraph(text)
self.assertEqual(len(enewick_graph.nodes()), 93)
enewick_phylo = enewick_to_phylonet(text)
self.assertEqual(len(enewick_phylo.nodes()), 93)
def test_three(self):
text = "((4, 5#1)2, (#1, 6)3);"
enewick_graph = enewick_to_digraph(text)
self.assertEqual(len(enewick_graph.nodes()), 6)
enewick_graph = calc_hybrid(enewick_graph)
leafs = get_leaf_nodes(enewick_graph)
gold_leafs = ['1', '4', '6', ]
self.assertItemsEqual(leafs, gold_leafs)
clusters = ["1,2", "2,3"]
gold = construct(clusters)
g = enewick_to_phylonet(text)
GM = GraphMatcher(g, gold)
self.assertTrue(GM.is_isomorphic())
def test_two(self):
text = "((4, 5#1)2, (#1, 6)3);"
enewick_graph = enewick_to_digraph(text)
self.assertEqual(len(enewick_graph.nodes()), 6)
enewick_phylo = enewick_to_phylonet(text)
gold_hard = "1,4 1,4,6 1,6 4 6".split()
hard = cluster_hard(enewick_graph)
self.assertItemsEqual(hard, gold_hard)
self.assertEqual(len(enewick_phylo.nodes()), 7)
clusters = [(1, 2), (2, 3),]
gold = construct(clusters)
GM = GraphMatcher(enewick_phylo, gold)
self.assertTrue(GM.is_isomorphic())
def test_one(self):
text = "((MOUSE,(HUMAN,RAT)),CIOIN);"
enewick_graph = enewick_to_digraph(text)
self.assertEqual(len(enewick_graph.nodes()), 7)
enewick_graph = enewick_to_phylonet(text)
self.assertEqual(len(enewick_graph.nodes()), 7)
clusters = [(1, 2, 3), (2, 3), (4,)]
gold = construct(clusters)
GM = GraphMatcher(enewick_graph, gold)
self.assertTrue(GM.is_isomorphic())
gold_hard = [
'CIOIN,HUMAN,MOUSE,RAT',
'CIOIN', 'HUMAN', 'MOUSE', 'RAT',
'HUMAN,MOUSE,RAT',
'HUMAN,RAT',
]
hard = cluster_hard(enewick_graph)
self.assertEqual(len(hard), 7)
self.assertItemsEqual(hard, gold_hard)
