def _get_mutation_positions(self, start):
amr_seq = self.get_amr_gene_seq()
genome_seq = self.get_genome_contig_hsp_seq()
# @formatter:off
return [
NucleotideMutationPosition(i, amr_seq, genome_seq, start)
for i in self._get_match_positions()
]
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')