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')
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')