def _get_abricate_vir(self):
self.virulence_table = run_abricate(
fasta=self.fasta,
db=self.db,
min_identity=self.min_identity,
min_coverage=self.min_coverage,
)
self.virulence_table['gene'] = [
gene.split('_')[0] for gene in self.virulence_table['gene']
]
return list(set(self.virulence_table['gene'])), self._get_pvl_status()
def _get_plasmidfinder(self):
self.plasmid_table = run_abricate(
fasta=self.fasta,
db=self.db,
min_identity=self.min_identity,
min_coverage=self.min_coverage,
)
self.plasmid_table['gene'] = [
gene.split('_')[0] for gene in self.plasmid_table['gene']
]
return list(set(self.plasmid_table['gene']))
def _get_acquired_resistance(self):
self.acquired_table = run_abricate(
fasta=self.fasta,
db=self.db,
min_identity=self.min_identity,
min_coverage=self.min_coverage,
)
self.acquired_table['gene'] = [
gene.split('_')[0] for gene in self.acquired_table['gene']
]
return self.acquired_table['gene'].to_list(), self._get_type_status()
def _get_acquired_resistance(self):
self.acquired_table = run_abricate(
fasta=self.fasta,
db=self.db,
min_identity=self.min_identity,
min_coverage=self.min_coverage,
)
products = self.acquired_table['product'].unique().tolist()
phenotypes = []
for res in self.acquired_table['resistance']:
for r in res.split(';'):
if r not in phenotypes:
phenotypes.append(r)
return products, self._get_type_status(), sorted(phenotypes)