def test_tuple_row(self):
row = (
"species-3",
"locus-mt",
"0.25",
"4.0",
"5",
"4",
"11.423634",
"587",
"0.227487",
"0.222071",
"0.259081",
"../sequences/species-3-locus-mt.fasta",
)
ac = AlignmentConfig(row)
self.assertEqual(ac.taxon_name, "species-3")
self.assertEqual(ac.locus_name, "locus-mt")
self.assertEqual(ac.ploidy_multiplier, 0.25)
self.assertEqual(ac.mutation_rate_multiplier, 4.0)
self.assertEqual(ac.number_of_gene_copies, (5, 4))
self.assertEqual(ac.kappa, 11.423634)
self.assertEqual(ac.length, 587)
self.assertEqual(ac.base_frequencies, (0.227487, 0.222071, 0.259081))
self.assertEqual(ac.path, "../sequences/species-3-locus-mt.fasta")
self.assertEqual([str(x) for x in ac.get_sample_table_row_elements()], list(row))
self.assertEqual(str(ac), "\t".join(row))
def test_equality(self):
row1 = (
"species-3",
"locus-mt",
"0.25",
"4.0",
"5",
"4",
"11.423634",
"587",
"0.227487",
"0.222071",
"0.259081",
"../sequences/species-3-locus-mt.fasta",
)
ac1 = AlignmentConfig(row1)
ac2 = AlignmentConfig(row1)
self.assertFalse(ac1 == ac2)
self.assertTrue(ac1.equals(ac2))
row2 = (
"species-3",
"locus-mt",
"0.25",
"4.0",
"5",
"4",
"11.423633",
"587",
"0.227487",
"0.222071",
"0.259082",
"../sequences/species-3-locus-mt.fasta",
)
ac3 = AlignmentConfig(row2)
self.assertFalse(ac1.equals(ac3))
def test_tuple_row(self):
row = ("species-3", "locus-mt", "0.25", "4.0", "5", "4", "11.423634",
"587", "0.227487", "0.222071", "0.259081",
"../sequences/species-3-locus-mt.fasta")
ac = AlignmentConfig(row)
self.assertEqual(ac.taxon_name, "species-3")
self.assertEqual(ac.locus_name, "locus-mt")
self.assertEqual(ac.ploidy_multiplier, 0.25)
self.assertEqual(ac.mutation_rate_multiplier, 4.0)
self.assertEqual(ac.number_of_gene_copies, (5, 4))
self.assertEqual(ac.kappa, 11.423634)
self.assertEqual(ac.length, 587)
self.assertEqual(ac.base_frequencies, (0.227487, 0.222071, 0.259081))
self.assertEqual(ac.path, "../sequences/species-3-locus-mt.fasta")
self.assertEqual([str(x) for x in ac.get_sample_table_row_elements()],
list(row))
self.assertEqual(str(ac), '\t'.join(row))
def test_string_row(self):
row = ("species-3\tlocus-mt\t0.25\t4.0\t5\t4\t11.423634\t587\t0.227487"
"\t0.222071\t0.259081\t../sequences/species-3-locus-mt.fasta")
ac = AlignmentConfig(row)
self.assertEqual(ac.taxon_name, "species-3")
self.assertEqual(ac.locus_name, "locus-mt")
self.assertEqual(ac.ploidy_multiplier, 0.25)
self.assertEqual(ac.mutation_rate_multiplier, 4.0)
self.assertEqual(ac.number_of_gene_copies, (5, 4))
self.assertEqual(ac.kappa, 11.423634)
self.assertEqual(ac.length, 587)
self.assertEqual(ac.base_frequencies, (0.227487, 0.222071, 0.259081))
self.assertEqual(ac.path, "../sequences/species-3-locus-mt.fasta")
self.assertEqual(str(ac), row)
def test_equality(self):
row1 = ("species-3", "locus-mt", "0.25", "4.0", "5", "4", "11.423634",
"587", "0.227487", "0.222071", "0.259081",
"../sequences/species-3-locus-mt.fasta")
ac1 = AlignmentConfig(row1)
ac2 = AlignmentConfig(row1)
self.assertFalse(ac1 == ac2)
self.assertTrue(ac1.equals(ac2))
row2 = ("species-3", "locus-mt", "0.25", "4.0", "5", "4", "11.423633",
"587", "0.227487", "0.222071", "0.259082",
"../sequences/species-3-locus-mt.fasta")
ac3 = AlignmentConfig(row2)
self.assertFalse(ac1.equals(ac3))