def testMutationPositionGapReferenceStartMiddleEnd(self):
mutation_position = 3
# @formatter:off
database_amr_gene_string = "CCC---GAC"
input_genome_string = "CCCATCGAC"
# @formatter:on
# @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')
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(), 'del',
'Incorrect query amino acid')
self.assertEqual(mutation.get_mutation_string_short(), 'I2del',
'Incorrect string')
def testMutationPositionGapReferenceEnd(self):
mutation_position = 2
# @formatter:off
database_amr_gene_string = "AT-G"
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(), 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(), 'AT-',
'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(), 'ins1I',
'Incorrect string')
def testMutationPositionMiddleCodon1(self):
mutation_position = 1
# @formatter:off
database_amr_gene_string = "ATCGATCGA"
input_genome_string = "AGCGATCGA"
# @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(), 'ATC',
'Incorrect database codon')
self.assertEqual(mutation.get_input_genome_codon(), 'AGC',
'Incorrect query codon')
self.assertEqual(mutation.get_database_amr_gene_mutation(), 'I',
'Incorrect database amino acid')
self.assertEqual(mutation.get_input_genome_mutation(), 'S',
'Incorrect query amino acid')
self.assertEqual(mutation.get_mutation_string_short(), 'I1S',
'Incorrect string')
def testMutationPositionStartCodon1Stop(self):
mutation_position = 2
# @formatter:off
database_amr_gene_string = "TACGATCGA"
input_genome_string = "TAAGATCGA"
# @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(), 'TAC',
'Incorrect database codon')
self.assertEqual(mutation.get_input_genome_codon(), 'TAA',
'Incorrect query codon')
self.assertEqual(mutation.get_database_amr_gene_mutation(), 'Y',
'Incorrect database amino acid')
self.assertEqual(mutation.get_input_genome_mutation(), '*',
'Incorrect query amino acid')
self.assertEqual(mutation.get_mutation_string_short(), 'Y1*',
'Incorrect string')
def testMutationPositionStartCodon3(self):
mutation_position = 6
# @formatter:off
database_amr_gene_string = "ATCGATCGA"
input_genome_string = "ATCGATGGA"
# @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(), 7,
'Incorrect nucleotide position')
self.assertEqual(mutation.get_codon_start(), 3,
'Incorrect codon start')
self.assertEqual(mutation.get_mutation_position(), 3,
'Incorrect mutation start')
self.assertEqual(mutation.get_database_amr_gene_codon(), 'CGA',
'Incorrect database codon')
self.assertEqual(mutation.get_input_genome_codon(), 'GGA',
'Incorrect query codon')
self.assertEqual(mutation.get_database_amr_gene_mutation(), 'R',
'Incorrect database amino acid')
self.assertEqual(mutation.get_input_genome_mutation(), 'G',
'Incorrect query amino acid')
self.assertEqual(mutation.get_mutation_string_short(), 'R3G',
'Incorrect string')
def testMutationPositionEndCodon2(self):
mutation_position = 5
# @formatter:off
database_amr_gene_string = "ATCGATCGA"
input_genome_string = "ATCGACCGA"
# @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(), 6,
'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(), 'GAC',
'Incorrect query codon')
self.assertEqual(mutation.get_database_amr_gene_mutation(), 'D',
'Incorrect database amino acid')
self.assertEqual(mutation.get_input_genome_mutation(), 'D',
'Incorrect query amino acid')
self.assertEqual(mutation.get_mutation_string_short(), 'D2D',
'Incorrect string')
def _get_mutation_positions(self, start):
amr_seq = self.get_amr_gene_seq()
genome_seq = self.get_genome_contig_hsp_seq()
# @formatter:off
return [
CodonMutationPosition(i, amr_seq, genome_seq, start)
for i in self._get_match_positions()
]
def testGetResistanceCodons1MutationStartCodon(self):
mutation_position = 0
amr_gene_string = "ATCGATCGA"
genome_string = "ATGGATCGA"
amr_gene_start = 1
mutation_start_methionine = CodonMutationPosition(
mutation_position, amr_gene_string, genome_string, amr_gene_start)
resistance_mutations = self.database.get_resistance_codons(
'gyrA', [mutation_start_methionine])
self.assertEqual(resistance_mutations, [],
"Did not pick up correct mutations")
def setUp(self):
pandas_pointfinder_table = pd.DataFrame([
['gyrA', 'gyrA', 1, 1, 'ATC', 'I', 'F', 'Quinolones', 15848289],
['gyrA', 'gyrA', 1, 2, 'GAT', 'D', 'N,H', 'Quinolones', 15848289],
],
columns=(
'#Gene_ID', 'Gene_name',
'No of mutations needed',
'Codon_pos', 'Ref_nuc',
'Ref_codon', 'Res_codon',
'Resistance', 'PMID'))
self.database = PointfinderDatabaseInfo.from_pandas_table(
pandas_pointfinder_table)
mutation_position = 0
amr_gene_string = "ATCGATCGA"
genome_string = "TTCGATCGA"
amr_gene_start = 1
self.mutation1 = CodonMutationPosition(mutation_position,
amr_gene_string, genome_string,
amr_gene_start)
mutation_position = 3
amr_gene_string = "ATCGATCGA"
genome_string = "ATCAATCGA"
amr_gene_start = 1
self.mutation2 = CodonMutationPosition(mutation_position,
amr_gene_string, genome_string,
amr_gene_start)
mutation_position = 8
amr_gene_string = "ATCGATCGA"
genome_string = "ATCGATCGT"
amr_gene_start = 1
self.mutation_missing = CodonMutationPosition(mutation_position,
amr_gene_string,
genome_string,
amr_gene_start)
def testGetResistanceCodons1MutationAANotMatch(self):
mutation_position = 3
amr_gene_string = "ATCGATCGA"
genome_string = "ATCGAACGA"
amr_gene_start = 1
mutation_aa_not_match = CodonMutationPosition(mutation_position,
amr_gene_string,
genome_string,
amr_gene_start)
resistance_mutations = self.database.get_resistance_codons(
'gyrA', [mutation_aa_not_match])
self.assertEqual(resistance_mutations, [],
"Did not pick up correct mutations")
def _get_mutation_positions(self, start):
mutation_positions_filtered = []
codon_starts = []
amr_seq = self.get_amr_gene_seq()
genome_seq = self.get_genome_contig_hsp_seq()
# Only return mutation position objects with unique codon start positions
mutation_positions = [
CodonMutationPosition(i, amr_seq, genome_seq, start)
for i in self._get_match_positions()
]
for m in mutation_positions:
if m._codon_start not in codon_starts:
codon_starts.append(m._codon_start)
mutation_positions_filtered.append(m)
# @formatter:off
return mutation_positions_filtered
