def testMutationPositionStartCodon2(self):
        mutation_position = 3
        # @formatter:off
        database_amr_gene_string = "ATCGATCGA"
        input_genome_string = "ATCAATCGA"
        #@formatter:on
        amr_gene_start = 1

        mutation = CodonMutationPosition(mutation_position,
                                         database_amr_gene_string,
                                         input_genome_string, amr_gene_start)

        self.assertEqual(mutation.get_nucleotide_position(), 4,
                         'Incorrect nucleotide position')
        self.assertEqual(mutation.get_codon_start(), 2,
                         'Incorrect codon start')
        self.assertEqual(mutation.get_mutation_position(), 2,
                         'Incorrect mutation start')
        self.assertEqual(mutation.get_database_amr_gene_codon(), 'GAT',
                         'Incorrect database codon')
        self.assertEqual(mutation.get_input_genome_codon(), 'AAT',
                         'Incorrect query codon')
        self.assertEqual(mutation.get_database_amr_gene_mutation(), 'D',
                         'Incorrect database amino acid')
        self.assertEqual(mutation.get_input_genome_mutation(), 'N',
                         'Incorrect query amino acid')
        self.assertEqual(mutation.get_mutation_string_short(), 'D2N',
                         'Incorrect string')
    def testMutationPositionEndCodon1(self):
        mutation_position = 2
        # @formatter:off
        database_amr_gene_string = "ATCGATCGA"
        input_genome_string = "ATGGATCGA"
        #@formatter:on
        amr_gene_start = 1

        mutation = CodonMutationPosition(mutation_position,
                                         database_amr_gene_string,
                                         input_genome_string, amr_gene_start)

        self.assertEqual(mutation.get_nucleotide_position(), 3,
                         'Incorrect nucleotide position')
        self.assertEqual(mutation.get_codon_start(), 1,
                         'Incorrect codon start')
        self.assertEqual(mutation.get_mutation_position(), 1,
                         'Incorrect mutation start')
        self.assertEqual(mutation.get_database_amr_gene_codon(), 'ATC',
                         'Incorrect database codon')
        self.assertEqual(mutation.get_input_genome_codon(), 'ATG',
                         'Incorrect query codon')
        self.assertEqual(mutation.get_database_amr_gene_mutation(), 'I',
                         'Incorrect database amino acid')
        self.assertEqual(mutation.get_input_genome_mutation(), 'M',
                         'Incorrect query amino acid')
        self.assertEqual(mutation.get_mutation_string_short(), 'I1M',
                         'Incorrect string')
    def testMutationPositionGapBeforeAfter(self):
        mutation_position = 3
        # @formatter:off
        database_amr_gene_string = "CCCATCGACT"
        input_genome_string = "-CCA--GA-T"
        #@formatter:on
        amr_gene_start = 1

        mutation = CodonMutationPosition(mutation_position,
                                         database_amr_gene_string,
                                         input_genome_string, amr_gene_start)

        self.assertEqual(mutation.get_nucleotide_position(), 4,
                         'Incorrect nucleotide position')
        self.assertEqual(mutation.get_codon_start(), 2,
                         'Incorrect codon start')
        self.assertEqual(mutation.get_mutation_position(), 2,
                         'Incorrect mutation start')
        self.assertEqual(mutation.get_database_amr_gene_codon(), 'ATC',
                         'Incorrect database codon')
        self.assertEqual(mutation.get_input_genome_codon(), 'A--',
                         'Incorrect query codon')
        self.assertEqual(mutation.get_database_amr_gene_mutation(), 'I',
                         'Incorrect database amino acid')
        self.assertEqual(mutation.get_input_genome_mutation(), 'X',
                         'Incorrect query amino acid')
        self.assertEqual(mutation.get_mutation_string_short(), 'I2X',
                         'Incorrect string')
    def testMutationPositionGapReferenceMiddle(self):
        mutation_position = 1
        # @formatter:off
        database_amr_gene_string = "A-CG"
        input_genome_string = "ATCG"
        #@formatter:on
        amr_gene_start = 1

        mutation = CodonMutationPosition(mutation_position,
                                         database_amr_gene_string,
                                         input_genome_string, amr_gene_start)

        self.assertEqual(mutation.get_nucleotide_position(), 2,
                         'Incorrect nucleotide position')
        self.assertEqual(mutation.get_codon_start(), 1,
                         'Incorrect codon start')
        self.assertEqual(mutation.get_mutation_position(), 1,
                         'Incorrect mutation start')
        self.assertEqual(mutation.get_database_amr_gene_codon(), 'A-C',
                         'Incorrect database codon')
        self.assertEqual(mutation.get_input_genome_codon(), 'ATC',
                         'Incorrect query codon')
        self.assertEqual(mutation.get_database_amr_gene_mutation(), 'X',
                         'Incorrect database amino acid')
        self.assertEqual(mutation.get_input_genome_mutation(), 'I',
                         'Incorrect query amino acid')
        self.assertEqual(mutation.get_mutation_string_short(), 'X1I',
                         'Incorrect string')
예제 #5
0
    def testMutationPositionGapReferenceLargerPreviousCodon(self):
        mutation_position = 3
        # @formatter:off
        database_amr_gene_string = "C-----GACTT"
        input_genome_string = "CCCATCGACTT"
        # @formatter:on
        amr_gene_start = 1

        mutation = CodonMutationPosition(mutation_position,
                                         database_amr_gene_string,
                                         input_genome_string, amr_gene_start)

        self.assertEqual(mutation.get_nucleotide_position(), 4,
                         'Incorrect nucleotide position')
        self.assertEqual(mutation.get_codon_start(), 2,
                         'Incorrect codon start')
        self.assertEqual(mutation.get_mutation_position(), 2,
                         'Incorrect mutation start')
        self.assertEqual(mutation.get_database_amr_gene_codon(), '---',
                         'Incorrect database codon')
        self.assertEqual(mutation.get_input_genome_codon(), 'ATC',
                         'Incorrect query codon')
        self.assertEqual(mutation.get_database_amr_gene_mutation(), 'ins',
                         'Incorrect database amino acid')
        self.assertEqual(mutation.get_input_genome_mutation(), 'I',
                         'Incorrect query amino acid')
        self.assertEqual(mutation.get_mutation_string_short(), 'ins2I',
                         'Incorrect string')