Python khmer.LabelHash类代码示例

def test_n_labels():
    lh = LabelHash(20, 1e7, 4)
    filename = utils.get_test_data('test-labels.fa')
    lh.consume_fasta_and_tag_with_labels(filename)

    print(lh.n_labels())
    assert lh.n_labels() == 4

def test_sweep_label_neighborhood():
    lb = LabelHash(20, 1e7, 4)
    filename = utils.get_test_data('single-read.fq')
    lb.consume_fasta_and_tag_with_labels(filename)

    labels = lb.sweep_label_neighborhood('CAGGCGCCCACCACCGTGCCCTCCAACCTGATGGT')
    assert len(labels) == 1
    assert labels.pop() == 0

def test_sweep_tag_neighborhood():
    lb = LabelHash(20, 1e7, 4)
    filename = utils.get_test_data('single-read.fq')
    lb.consume_fasta_and_tag(filename)

    tags = lb.sweep_tag_neighborhood('CAGGCGCCCACCACCGTGCCCTCCAACCTGATGGT')
    assert len(tags) == 1
    assert tags.pop() == 173473779682

def test_get_tag_labels():
    lb = LabelHash(20, 1e7, 4)
    filename = utils.get_test_data('single-read.fq')
    lb.consume_fasta_and_tag_with_labels(filename)
    tag = 173473779682

    labels = lb.get_tag_labels(tag)
    assert len(labels) == 1
    assert labels.pop() == 0

def test_get_label_dict():
    lb = LabelHash(20, 1e7, 4)
    filename = utils.get_test_data('test-labels.fa')
    lb.consume_fasta_and_tag_with_labels(filename)

    labels = lb.get_label_dict()
    expected = [0, 1, 2, 3]
    for e_label in expected:
        assert e_label in labels
    for a_label in labels:
        assert a_label in expected

def test_consume_sequence_and_tag_with_labels():
    lb = LabelHash(20, 1e6, 4)
    label = 0
    sequence = 'ATGCATCGATCGATCGATCGATCGATCGATCGATCGATCG'

    n_consumed = lb.consume_sequence_and_tag_with_labels(sequence, label)
    labels = set()
    labels.update(lb.sweep_label_neighborhood(sequence))

    assert label in labels
    assert len(labels) == 1

def test_load_wrong_fileversion():
    lb = LabelHash(20, 1e7, 4)

    # try to load a tagset from an old version
    filename = utils.get_test_data('badversion-k32.tagset')
    try:
        lb.load_labels_and_tags(filename)
        assert 0, "this should not succeed - bad file type"
    except OSError as err:
        print(str(err))
        assert "Incorrect file format version" in str(err)

def test_save_load_corrupted():
    lb_pre = LabelHash(20, 1e7, 4)
    filename = utils.get_test_data('test-labels.fa')
    lb_pre.consume_fasta_and_tag_with_labels(filename)

    # save labels to a file
    savepath = utils.get_temp_filename('saved.labels')
    lb_pre.save_labels_and_tags(savepath)

    # trash the old LabelHash
    del lb_pre

    lb = LabelHash(20, 1e7, 4)

    # produce all possible truncated versions of this file
    data = open(savepath, 'rb').read()
    for i in range(len(data)):
        truncated = utils.get_temp_filename('trunc.labels')
        fp = open(truncated, 'wb')
        fp.write(data[:i])
        fp.close()

        try:
            lb.load_labels_and_tags(truncated)
            assert 0, "this should not succeed -- truncated file len %d" % (i,)
        except OSError as err:
            print('expected failure for', i, ': ', str(err))

def test_consume_partitioned_fasta_and_tag_with_labels():
    lb = LabelHash(20, 1e7, 4)
    filename = utils.get_test_data('real-partition-small.fa')

    total_reads, n_consumed = lb.consume_partitioned_fasta_and_tag_with_labels(
        filename)
    labels = set()
    for record in screed.open(filename):
        seq = record.sequence
        labels.update(lb.sweep_label_neighborhood(seq, 0, False, False))
    # print lb.n_labels()
    # print labels
    assert len(labels) == 1
    assert labels.pop() == 2
    assert lb.n_labels() == 1

def test_save_fail_readonly():
    lb_pre = LabelHash(20, 1e7, 4)
    filename = utils.get_test_data('test-labels.fa')
    lb_pre.consume_fasta_and_tag_with_labels(filename)

    # save labels to a file
    savepath = utils.get_temp_filename('saved.labels')
    fp = open(savepath, 'w')
    fp.close()

    os.chmod(savepath, 0x444)

    try:
        lb_pre.save_labels_and_tags(savepath)
        assert 0, "this should fail: read-only file"
    except OSError as err:
        print(str(err))

def test_load_wrong_filetype():
    lb = LabelHash(20, 1e7, 4)

    # try to load a tagset
    filename = utils.get_test_data('goodversion-k32.tagset')
    try:
        lb.load_labels_and_tags(filename)
        assert 0, "this should not succeed - bad file type"
    except OSError as err:
        print(str(err))
        assert "Incorrect file format type" in str(err)

    # try to load a nonsense file
    filename = utils.get_test_data('all-A.fa')
    try:
        lb.load_labels_and_tags(filename)
        assert 0, "this should not succeed - bad file signature"
    except OSError as err:
        print(str(err))
        assert "Incorrect file signature" in str(err)

def test_label_tag_correctness():
    lb = LabelHash(20, 1e7, 4)
    filename = utils.get_test_data('test-labels.fa')
    lb.consume_fasta_and_tag_with_labels(filename)

    # read A
    labels = lb.sweep_label_neighborhood(
        'ATCGTGTAAGCTATCGTAATCGTAAGCTCTGCCTAGAGCTAGGCTAGGCTCTGCCTAGAG'
        'CTAGGCTAGGTGTGCTCTGCCTAGAGCTAGGCTAGGTGT')
    print lb.sweep_tag_neighborhood(
        'TTCGTGTAAGCTATCGTAATCGTAAGCTCTGCCTAGAGCTAGGCTAGGCTCTGCCTAGAG'
        'CTAGGCTAGGTGTGCTCTGCTAGAGCTAGGCTAGGTGT')
    print labels
    print len('ATCGTGTAAGCTATCGTAATCGTAAGCTCTGCCTAGAGCTAGGCTAG') - 19
    assert len(labels) == 2
    assert 0 in labels
    assert 1 in labels

    # read B
    labels = lb.sweep_label_neighborhood(
        'GCGTAATCGTAAGCTCTGCCTAGAGCTAGGCTAGCTCTGCCTAGAGCTAGGCTAGGTGTTGGGGATAG'
        'ATAGATAGATGACCTAGAGCTAGGCTAGGTGTTGGGGATAGATAGATAGATGA')
    print labels
    assert len(labels) == 3
    assert 0 in labels
    assert 1 in labels
    assert 2 in labels

    # read C
    labels = lb.sweep_label_neighborhood(
        'TGGGATAGATAGATAGATGACCTAGAGCTAGGCTAGGTGTTGGGGATAGATAGATAGATGACCTAGAG'
        'CTAGGCTAGGTGTTGGGGATAGATAGATAGATGAGTTGGGGATAGATAGATAGATGAGTGTAGATCCA'
        'ACAACACATACA')
    print labels
    assert len(labels) == 2
    assert 1 in labels
    assert 2 in labels

    # read D
    labels = lb.sweep_label_neighborhood(
        'TATATATATAGCTAGCTAGCTAACTAGCTAGCATCGATCGATCGATC')
    print labels
    assert len(labels) == 1
    assert 3 in labels

def test_get_label_dict_save_load():
    lb_pre = LabelHash(20, 1e7, 4)
    filename = utils.get_test_data('test-labels.fa')
    lb_pre.consume_fasta_and_tag_with_labels(filename)

    # save labels to a file
    savepath = utils.get_temp_filename('saved.labels')
    lb_pre.save_labels_and_tags(savepath)

    # trash the old LabelHash
    del lb_pre

    # create new, load labels & tags
    lb = LabelHash(20, 1e7, 4)
    lb.load_labels_and_tags(savepath)

    labels = lb.get_label_dict()
    expected = [0, 1, 2, 3]
    for e_label in expected:
        assert e_label in labels
    for a_label in labels:
        assert a_label in expected

def test_get_label_dict_save_load_wrong_ksize():
    lb_pre = LabelHash(19, 1e7, 4)
    filename = utils.get_test_data('test-labels.fa')
    lb_pre.consume_fasta_and_tag_with_labels(filename)

    # save labels to a file
    savepath = utils.get_temp_filename('saved.labels')
    lb_pre.save_labels_and_tags(savepath)

    # trash the old LabelHash
    del lb_pre

    # create new, load labels & tags
    lb = LabelHash(20, 1e7, 4)
    try:
        lb.load_labels_and_tags(savepath)
        assert 0, "this should not succeed - different ksize"
    except OSError as err:
        print(str(err))
        assert "Incorrect k-mer size 19" in str(err)

def test_consume_fasta_and_tag_with_labels():
    lb = LabelHash(20, 1e7, 4)
    read_1 = 'ACGTAACCGGTTAAACCCGGGTTTAAAACCCCGGGGTTTT'
    filename = utils.get_test_data('test-transcript.fa')

    total_reads, n_consumed = lb.consume_fasta_and_tag_with_labels(filename)
    print("doing get")
    assert lb.graph.get(read_1[:20])
    assert total_reads == 3
    print("doing n_labels")
    print(lb.n_labels())
    print("doing label dict")
    print(lb.get_label_dict())
    print("get tagset")
    for tag in lb.graph.get_tagset():
        print("forward hash")
        print(tag, khmer.forward_hash(tag, 20))
    for record in screed.open(filename):
        print("Sweeping tags")
        print(lb.sweep_tag_neighborhood(record.sequence, 40))
        print("Sweeping labels...")
        print(lb.sweep_label_neighborhood(record.sequence, 40))
    assert lb.n_labels() == 3