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