def testMutationPositionGapReference(self): mutation_position = 0 # @formatter:off database_amr_gene_string = "-TCG" input_genome_string = "ATCG" # @formatter:on amr_gene_start = 1 mutation = NucleotideMutationPosition(mutation_position, database_amr_gene_string, input_genome_string, amr_gene_start) self.assertEqual(mutation.get_mutation_position(), 1, 'Incorrect nucleotide position') self.assertEqual(mutation.get_database_amr_gene_mutation(), '-', 'Incorrect database mutation') self.assertEqual(mutation.get_input_genome_mutation(), 'A', 'Incorrect query mutation') self.assertEqual(mutation.get_mutation_string_short(), '-1A', 'Incorrect string')
def testMutationPositionNucleotideEnd(self): mutation_position = 8 # @formatter:off database_amr_gene_string = "ATCGATCGA" input_genome_string = "ATCGATCGG" # @formatter:on amr_gene_start = 1 mutation = NucleotideMutationPosition(mutation_position, database_amr_gene_string, input_genome_string, amr_gene_start) self.assertEqual(mutation.get_mutation_position(), 9, 'Incorrect nucleotide position') self.assertEqual(mutation.get_database_amr_gene_mutation(), 'A', 'Incorrect database mutation') self.assertEqual(mutation.get_input_genome_mutation(), 'G', 'Incorrect query mutation') self.assertEqual(mutation.get_mutation_string_short(), 'A9G', 'Incorrect string')