def virulence(self):
"""
Virulence gene detection
"""
virulence = BLAST(args=self, analysistype='virulence')
virulence.seekr()
metadataprinter.MetadataPrinter(inputobject=self)
def resfinder(self):
"""
Resistance finding - assemblies
"""
resfinder = BLAST(args=self, analysistype='resfinder_assembled')
resfinder.seekr()
metadataprinter.MetadataPrinter(inputobject=self)
def geneseekr(self):
"""
Find genes of interest
"""
geneseekr = BLAST(args=self, analysistype='genesippr', cutoff=95)
geneseekr.seekr()
metadataprinter.MetadataPrinter(inputobject=self)
def sixteens(self):
"""
Run the 16S analyses
"""
sixteen_s = BLAST(args=self, analysistype='sixteens_full', cutoff=95)
sixteen_s.seekr()
metadataprinter.MetadataPrinter(inputobject=self)
def rmlst_assembled(self):
"""
Run rMLST analyses on assemblies
"""
if not os.path.isfile(os.path.join(self.reportpath, 'rmlst.csv')):
rmlst = BLAST(args=self, analysistype='rmlst', cutoff=100)
rmlst.seekr()
else:
parse = ReportParse(args=self, analysistype='rmlst')
parse.report_parse()
metadataprinter.MetadataPrinter(inputobject=self)
def serosippr(self):
"""
Serotyping analyses
"""
# pipeline=True)
sero = BLAST(args=self,
analysistype='serosippr',
cutoff=90,
genus_specific=True,
unique=True)
sero.seekr()
metadataprinter.MetadataPrinter(inputobject=self)
def cgmlst_assembled(self):
"""
Run rMLST analyses on assemblies
"""
if os.path.isfile(os.path.join(self.reportpath, 'cgmlst.csv')):
parse = ReportParse(args=self, analysistype='cgmlst')
parse.report_parse()
else:
cgmlst = BLAST(args=self,
analysistype='cgMLST',
cutoff=100,
genus_specific=True)
cgmlst.seekr()
metadataprinter.MetadataPrinter(inputobject=self)