default.py 文件源码

def runAnalysis(bam, fasta, blastresults, taxdump, modelOutput, output, tokeep, toremove, binary, target, level):
    taxdump, taxidDict = common.parseTaxdump(taxdump, False)
    gc.collect()
    click.echo("Taxdump parsed, %d taxIDs loaded" % len(taxdump))
    contigs = readFasta(fasta)
    gc.collect()
    click.echo("FASTA loaded, %d contigs returned" % len(contigs))
    contigs = readBAM(bam, contigs)
    gc.collect()
    click.echo("BAM loaded")
    contigs, classMap, classList = readBLAST(blastresults,
                                             taxdump, level.lower(), contigs)
    gc.collect()
    click.echo("BLAST results loaded")
    corpus, testdata, features = common.constructCorpus(list(contigs.values()), classMap, binary, target)
    gc.collect()
    click.echo("Corpus constucted, %d contigs in corpus and %d contigs in test data" % (len(corpus), len(testdata)))
    classifier = common.constructModel(corpus, classList, features, modelOutput)
    result = common.classifyData(classifier, testdata, classMap)
    common.generateOutput(tokeep, toremove, result, contigs.values(), target, output)