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)