예제 #1
0
 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))
예제 #2
0
 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))
예제 #3
0
 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))
예제 #4
0
 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)
예제 #5
0
 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))