def test_join_nodes(self):
"""join them nodes! (((99 + 97) + 94) + 91) + ..."""
parsed = [make_nodes(self.clst_99, 0.01, 99),
make_nodes(self.clst_97, 0.02, 97),
make_nodes(self.clst_94, 0.03, 94)]
exp = """((((3:.005)99_2_3:.01,(8:.005,7:.005)99_3_8:.01)97_0_3:.015)94_0_3,
(((1:.005,6:.005)99_1_1:.01)97_1_1:.015,
((10:.005,20:.005,30:.005)99_0_10:.01)97_2_10:.015)94_1_1);"""
expt = DndParser(exp)
obs = join_nodes(parsed)
self.assertEqual(obs.getNewick(with_distances=True),
expt.getNewick(with_distances=True))
def test_join_nodes(self):
"""join them nodes! (((99 + 97) + 94) + 91) + ..."""
parsed = [
make_nodes(self.clst_99, 0.01, 99),
make_nodes(self.clst_97, 0.02, 97),
make_nodes(self.clst_94, 0.03, 94)
]
exp = """((((3:.005)99_2_3:.01,(8:.005,7:.005)99_3_8:.01)97_0_3:.015)94_0_3,
(((1:.005,6:.005)99_1_1:.01)97_1_1:.015,
((10:.005,20:.005,30:.005)99_0_10:.01)97_2_10:.015)94_1_1);"""
expt = DndParser(exp)
obs = join_nodes(parsed)
self.assertEqual(obs.getNewick(with_distances=True),
expt.getNewick(with_distances=True))
def test_make_nodes(self):
"""makes nodes..."""
exp_99_0_10 = PhyloNode(Name="10", Length=0.005)
exp_99_0_20 = PhyloNode(Name="20", Length=0.005)
exp_99_0_30 = PhyloNode(Name="30", Length=0.005)
exp_99_0 = PhyloNode(Name="99_0_10",Length=None, Children=\
[exp_99_0_10,exp_99_0_20,exp_99_0_30])
exp_99_1_1 = PhyloNode(Name="1", Length=0.005)
exp_99_1_6 = PhyloNode(Name="6", Length=0.005)
exp_99_1 = PhyloNode(Name="99_1_1",Length=None, Children=\
[exp_99_1_1,exp_99_1_6])
exp_99_2_3 = PhyloNode(Name="3", Length=0.005)
exp_99_2 = PhyloNode(Name="99_2_3", Length=None, Children=[exp_99_2_3])
exp_99_3_8 = PhyloNode(Name="8", Length=0.005)
exp_99_3_7 = PhyloNode(Name="7", Length=0.005)
exp_99_3 = PhyloNode(Name="99_3_8", Length=None, Children=\
[exp_99_3_8,exp_99_3_7])
exp_lookup = {
'10': exp_99_0,
'1': exp_99_1,
'3': exp_99_2,
'8': exp_99_3
}
lookup, nodes = make_nodes(self.clst_99, 0.01, 99)
self.assertEqual(nodes[0].getNewick(with_distances=True),
exp_99_0.getNewick(with_distances=True))
self.assertEqual(nodes[1].getNewick(with_distances=True),
exp_99_1.getNewick(with_distances=True))
self.assertEqual(nodes[2].getNewick(with_distances=True),
exp_99_2.getNewick(with_distances=True))
self.assertEqual(nodes[3].getNewick(with_distances=True),
exp_99_3.getNewick(with_distances=True))
self.assertEqual(len(nodes), 4)
self.assertEqual(lookup.keys(), exp_lookup.keys())
self.assertEqual(map(str, lookup.values()),
map(str, exp_lookup.values()))
def test_make_nodes(self):
"""makes nodes..."""
exp_99_0_10 = PhyloNode(Name="10",Length=0.005)
exp_99_0_20 = PhyloNode(Name="20",Length=0.005)
exp_99_0_30 = PhyloNode(Name="30",Length=0.005)
exp_99_0 = PhyloNode(Name="99_0_10",Length=None, Children=\
[exp_99_0_10,exp_99_0_20,exp_99_0_30])
exp_99_1_1 = PhyloNode(Name="1",Length=0.005)
exp_99_1_6 = PhyloNode(Name="6",Length=0.005)
exp_99_1 = PhyloNode(Name="99_1_1",Length=None, Children=\
[exp_99_1_1,exp_99_1_6])
exp_99_2_3 = PhyloNode(Name="3", Length=0.005)
exp_99_2 = PhyloNode(Name="99_2_3", Length=None, Children=[exp_99_2_3])
exp_99_3_8 = PhyloNode(Name="8", Length=0.005)
exp_99_3_7 = PhyloNode(Name="7", Length=0.005)
exp_99_3 = PhyloNode(Name="99_3_8", Length=None, Children=\
[exp_99_3_8,exp_99_3_7])
exp_lookup = {'10':exp_99_0,'1':exp_99_1,'3':exp_99_2,'8':exp_99_3}
lookup, nodes = make_nodes(self.clst_99, 0.01, 99)
self.assertEqual(nodes[0].getNewick(with_distances=True),
exp_99_0.getNewick(with_distances=True))
self.assertEqual(nodes[1].getNewick(with_distances=True),
exp_99_1.getNewick(with_distances=True))
self.assertEqual(nodes[2].getNewick(with_distances=True),
exp_99_2.getNewick(with_distances=True))
self.assertEqual(nodes[3].getNewick(with_distances=True),
exp_99_3.getNewick(with_distances=True))
self.assertEqual(len(nodes), 4)
self.assertEqual(lookup.keys(), exp_lookup.keys())
self.assertEqual(map(str, lookup.values()),
map(str,exp_lookup.values()))
