Exemplos de classify em Python

Exemplo n.º 1

def test_kraken_classify(mocks, kraken, db, in_bam):
    out_reads = util.file.mkstempfname('.reads.txt')
    kraken.classify(in_bam, db, out_reads)
    args = mocks['check_call'].call_args[0][0]
    assert 'kraken' == os.path.basename(args[0])
    assert util.misc.list_contains(['--db', db], args)
    assert util.misc.list_contains(['--output', out_reads], args)
    assert util.misc.list_contains(['--threads', str(_CPUS)], args)

Exemplo n.º 2

Arquivo: test_tools_krakenuniq.py Projeto: broadinstitute/viral-ngs

def test_kraken_classify(mocks, kraken, db, in_bam):
    out_reads = util.file.mkstempfname('.reads.txt')
    kraken.classify(in_bam, db, out_reads)
    args = mocks['check_call'].call_args[0][0]
    assert 'kraken' == os.path.basename(args[0])
    assert util.misc.list_contains(['--db', db], args)
    assert util.misc.list_contains(['--output', out_reads], args)
    assert util.misc.list_contains(['--threads', str(_CPUS)], args)

Exemplo n.º 3

Arquivo: test_kraken.py Projeto: yesimon/viral-ngs

def test_kraken_tool(tmpdir, kraken, kraken_db, input_bam):
    outdir = tempfile.mkdtemp('-kraken')
    out = join(outdir, 'zaire_ebola.kraken')
    out_filtered = join(outdir, 'zaire_ebola.filtered-kraken')
    out_report = join(outdir, 'zaire_ebola.kraken-report')
    kraken.classify(input_bam, kraken_db, out)
    kraken.filter(out, kraken_db, out_filtered, 0.05)
    kraken.report(out_filtered, kraken_db, out_report)
    assert os.path.getsize(out_report) > 0
    assert os.path.getsize(out_filtered) > 0

Exemplo n.º 4

Arquivo: test_kraken.py Projeto: flyfl1992/viral-ngs

def test_kraken_tool(tmpdir, kraken, kraken_db, input_bam):
    outdir = tempfile.mkdtemp('-kraken')
    out = join(outdir, 'zaire_ebola.kraken')
    out_filtered = join(outdir, 'zaire_ebola.filtered-kraken')
    out_report = join(outdir, 'zaire_ebola.kraken-report')
    kraken.classify(input_bam, kraken_db, out)
    kraken.filter(out, kraken_db, out_filtered, 0.05)
    kraken.report(out_filtered, kraken_db, out_report)
    assert os.path.getsize(out_report) > 0
    assert os.path.getsize(out_filtered) > 0

Exemplo n.º 5

def test_classify_num_threads(mocks, kraken, db, in_bam):
    out_reads = util.file.mkstempfname('.reads.txt')

    kraken.classify(in_bam, db, out_reads)
    args = mocks['check_call'].call_args[0][0]
    assert 'kraken' == os.path.basename(args[0])
    assert '--threads' in args
    actual = args[args.index('--threads')+1]
    assert actual == str(_CPUS)

    for requested in (1,2,3,8,11,20):
        expected = min(_CPUS, requested)
        kraken.classify(in_bam, db, out_reads, numThreads=requested)
        args = mocks['check_call'].call_args[0][0]
        assert 'kraken' == os.path.basename(args[0])
        assert '--threads' in args
        actual = args[args.index('--threads')+1]
        assert actual == str(expected), "failure for requested %s, expected %s, actual %s" % (requested, expected, actual)

Exemplo n.º 6

Arquivo: test_tools_krakenuniq.py Projeto: broadinstitute/viral-ngs

def test_classify_num_threads(mocks, kraken, db, in_bam):
    out_reads = util.file.mkstempfname('.reads.txt')

    kraken.classify(in_bam, db, out_reads)
    args = mocks['check_call'].call_args[0][0]
    assert 'kraken' == os.path.basename(args[0])
    assert '--threads' in args
    actual = args[args.index('--threads')+1]
    assert actual == str(_CPUS)

    for requested in (1,2,3,8,11,20):
        expected = min(_CPUS, requested)
        kraken.classify(in_bam, db, out_reads, numThreads=requested)
        args = mocks['check_call'].call_args[0][0]
        assert 'kraken' == os.path.basename(args[0])
        assert '--threads' in args
        actual = args[args.index('--threads')+1]
        assert actual == str(expected), "failure for requested %s, expected %s, actual %s" % (requested, expected, actual)

Exemplo n.º 7

Arquivo: test_kraken.py Projeto: mypandos/viral-ngs

def test_kraken_tool(tmpdir, kraken, kraken_db, input_fastqs):
    outdir = tempfile.mkdtemp('-kraken')
    out = join(outdir, 'zaire_ebola.kraken')
    out_filtered = join(outdir, 'zaire_ebola.filtered-kraken')
    out_report = join(outdir, 'zaire_ebola.kraken-report')
    assert kraken.classify(kraken_db, input_fastqs, out).returncode == 0
    result = kraken.execute(
        'kraken-filter', kraken_db, out_filtered, [out],
        options={'--threshold': 0.05})
    assert result.returncode == 0
    result = kraken.execute(
        'kraken-report', kraken_db, out_report, [out_filtered])
    assert result.returncode == 0

    assert os.path.getsize(out_report) > 0
    assert os.path.getsize(out_filtered) > 0

Exemplo n.º 8

Arquivo: test_kraken.py Projeto: mamanambiya/viral-ngs

def test_kraken_tool(tmpdir, kraken, kraken_db, input_fastqs):
    outdir = tempfile.mkdtemp('-kraken')
    out = join(outdir, 'zaire_ebola.kraken')
    out_filtered = join(outdir, 'zaire_ebola.filtered-kraken')
    out_report = join(outdir, 'zaire_ebola.kraken-report')
    assert kraken.classify(kraken_db, input_fastqs, out).returncode == 0
    result = kraken.execute('kraken-filter',
                            kraken_db,
                            out_filtered, [out],
                            options={'--threshold': 0.05})
    assert result.returncode == 0
    result = kraken.execute('kraken-report', kraken_db, out_report,
                            [out_filtered])
    assert result.returncode == 0

    assert os.path.getsize(out_report) > 0
    assert os.path.getsize(out_filtered) > 0