def construct_network(comb):
left, right = comb
h_left = cluster_hard(left)
h_right = cluster_hard(right)
clusters = {cl for cl in itertools.chain(h_left, h_right)}
g = construct(clusters)
return g
def test_seven(self):
edges = [("['1', u'4', u'6']", u'3'),
("['1', u'4', u'6']", u'2'),
('1h', '1'),
(u'3', '1h'),
(u'3', u'6'),
(u'2', '1h'),
(u'2', u'4') ]
G = nx.DiGraph()
G.add_edges_from(edges)
gold = ['1', '4', '6', '1,4,6', '1,4', '1,6', ]
self.assertItemsEqual(cluster_hard(G), gold)
def test_five(self):
edges = [
((1, 2, 3, 4), (4, )),
((4, ), (3, )),
((1, 2,), (1, )),
((1, 2,), (2, )),
((1, 2, 3, 4), (1, 2, )),
]
G = nx.DiGraph()
G.add_edges_from(edges)
gold = "1 2 3 1,2 1,2,3".split()
self.assertItemsEqual(cluster_hard(G), gold)
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)
def test_four(self):
clusters = [(1, 2, 3)]
G = construct(clusters)
gold = "1 2 3 1,2,3".split()
self.assertItemsEqual(cluster_hard(G), gold)
def test_three(self):
clusters = [(1, 2), (3, 4)]
G = construct(clusters)
gold = "1 2 3 4 1,2,3,4 1,2 3,4".split()
self.assertItemsEqual(cluster_hard(G), gold)
def test_one(self):
clusters = [(1, 2)]
G = construct(clusters)
gold = "1 2 1,2".split()
self.assertItemsEqual(cluster_hard(G), gold)
def test_empty(self):
G = nx.DiGraph()
gold = set()
self.assertItemsEqual(cluster_hard(G), gold)