Python GraphLabels.consume_fasta_and_tag_with_labels方法代码示例

# 需要导入模块: from khmer import GraphLabels [as 别名]
# 或者: from khmer.GraphLabels import consume_fasta_and_tag_with_labels [as 别名]
def test_save_load_corrupted():
    lb_pre = GraphLabels(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 GraphLabels
    del lb_pre

    lb = GraphLabels(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))

# 需要导入模块: from khmer import GraphLabels [as 别名]
# 或者: from khmer.GraphLabels import consume_fasta_and_tag_with_labels [as 别名]
def test_n_labels():
    lh = GraphLabels(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

# 需要导入模块: from khmer import GraphLabels [as 别名]
# 或者: from khmer.GraphLabels import consume_fasta_and_tag_with_labels [as 别名]
def test_sweep_label_neighborhood():
    lb = GraphLabels(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

# 需要导入模块: from khmer import GraphLabels [as 别名]
# 或者: from khmer.GraphLabels import consume_fasta_and_tag_with_labels [as 别名]
def test_get_tag_labels():
    lb = GraphLabels(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

# 需要导入模块: from khmer import GraphLabels [as 别名]
# 或者: from khmer.GraphLabels import consume_fasta_and_tag_with_labels [as 别名]
def test_label_tag_correctness_save_load():
    lb_pre = GraphLabels(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 GraphLabels
    del lb_pre

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

    # 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

# 需要导入模块: from khmer import GraphLabels [as 别名]
# 或者: from khmer.GraphLabels import consume_fasta_and_tag_with_labels [as 别名]
def test_get_label_dict():
    lb = GraphLabels(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

# 需要导入模块: from khmer import GraphLabels [as 别名]
# 或者: from khmer.GraphLabels import consume_fasta_and_tag_with_labels [as 别名]
def test_save_fail_readonly():
    lb_pre = GraphLabels(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))

# 需要导入模块: from khmer import GraphLabels [as 别名]
# 或者: from khmer.GraphLabels import consume_fasta_and_tag_with_labels [as 别名]
def test_label_tag_correctness():
    lb = GraphLabels(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

# 需要导入模块: from khmer import GraphLabels [as 别名]
# 或者: from khmer.GraphLabels import consume_fasta_and_tag_with_labels [as 别名]
def test_get_label_dict_save_load_wrong_ksize():
    lb_pre = GraphLabels(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 GraphLabels
    del lb_pre

    # create new, load labels & tags
    lb = GraphLabels(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)

# 需要导入模块: from khmer import GraphLabels [as 别名]
# 或者: from khmer.GraphLabels import consume_fasta_and_tag_with_labels [as 别名]
def test_get_label_dict_save_load():
    lb_pre = GraphLabels(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 GraphLabels
    del lb_pre

    # create new, load labels & tags
    lb = GraphLabels(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

# 需要导入模块: from khmer import GraphLabels [as 别名]
# 或者: from khmer.GraphLabels import consume_fasta_and_tag_with_labels [as 别名]
def test_consume_fasta_and_tag_with_labels():
    lb = GraphLabels(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