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
