def test_parse_dna(self):
f = data_stream("nexus/dna.nex")
n = Nexus(f)
taxa = n.taxlabels
taxa.sort()
self.assertEqual(len(taxa), 10)
self.assertEqual(taxa[0], "Carp")
self.assertEqual(taxa[-1], "Whale")
f.close()
def test_parse_f0(self):
f = data_stream("nexus/test_Nexus_input.nex")
n = Nexus(f)
# self.output_basics(n)
expected = ['t1',
"t2 the name",
"isn'that [a] strange name?",
"one should be punished, for (that)!",
"t5", "t6", "t7", "t8", "t9"]
taxa = n.taxlabels
self.assertEqual(taxa, expected)
f.close()
def test_TreeTest1(self):
"""Test Tree module."""
f = data_stream("nexus/test_Nexus_input.nex")
n = Nexus(f)
t3 = n.trees[2]
n.trees[2]
t3.root_with_outgroup(["t1", "t5"])
# Return node_id of common ancestor if
# taxon_list is monophyletic, -1 otherwise.
self.assertEqual(t3.is_monophyletic(["t1", "t5"]), 13)
t3.split(parent_id=t3.search_taxon("t9"))
f.close()
def test_parse_protein(self):
f = data_stream("nexus/protein.nex")
Nexus(f)
f.close()
def test_create(self):
n = Nexus()
self.assertNotEqual(n, None)