def predict(self,**kw):
"""Predict host taxonomy for viral sequences.
Parameters are taken from self.opt.
@param predSeq Name of FASTA sequence file to classify
@param immDb Path to directory with IMMs
@param predOutDir Output directory for predictions
"""
sopt = self.opt
opt = copy(sopt)
opt.mode = "predict"
opt.inpSeq = sopt.predSeq
opt.outDir = sopt.predOutDir
immStore = ImmStore(opt.immDb)
immIds = immStore.listImmIds()
immIdsPath = pjoin(opt.outDir,"imm-ids.pkl")
rmrf(opt.outDir)
makedir(opt.outDir)
dumpObj(immIds,immIdsPath)
opt.immIds = immIdsPath
#opt.predMode = "host"
imm = ImmClassifierApp(opt=opt)
jobs = imm.run(**kw)
return jobs
def taxonomy_report(pred_out_taxa,out_dir="results",ncbi_taxonomy_dir=None):
pred_out_taxa = os.path.abspath(pred_out_taxa)
out_dir = os.path.abspath(out_dir)
if ncbi_taxonomy_dir:
ncbi_taxonomy_dir = os.path.abspath(ncbi_taxonomy_dir)
opt = Struct()
opt.runMode = "inproc"
opt.web = False
opt.needTerminator = False
opt.mode = "export-predictions"
opt.predOutDir = out_dir
opt.predOutTaxa = pred_out_taxa
opt.predMinLenSamp = 1
opt.skipPredOutTaxaCsv = 1
opt.taxaTreeNcbiDir = ncbi_taxonomy_dir
opt.predOutStatsKronaEmbed = "krona"
ImmClassifierApp.fillWithDefaultOptions(opt)
imm = ImmClassifierApp(opt=opt)
imm.run()
def _outScoreCombPath(klass,opt):
o = Struct(outDir=opt.predOutDir,mode="predict")
ImmClassifierApp.fillWithDefaultOptions(o)
return o.outScoreComb
