Python GraphLabels.consume_partitioned_fasta_and_tag_with_labels Beispiele

Beispiel #1

Datei: test_sequence_validation.py Projekt: betatim/khmer

def test_consume_partitioned_seqfile_and_label(Graphtype):
    infile = utils.get_test_data('valid-read-testing.fq')

    # read this in consume_and_tag
    graph = Graphtype(15, *params_1m)
    x = GraphLabels(graph)
    x.consume_partitioned_fasta_and_tag_with_labels(infile)

    assert x.n_labels == 9

Beispiel #2

def test_consume_partitioned_seqfile_and_label(Graphtype):
    infile = utils.get_test_data('valid-read-testing.fq')

    # read this in consume_and_tag
    graph = Graphtype(15, *params_1m)
    x = GraphLabels(graph)
    x.consume_partitioned_fasta_and_tag_with_labels(infile)

    assert x.n_labels == 9

Beispiel #3

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

    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

Beispiel #4

Datei: test_labelhash.py Projekt: wltrimbl/khmer

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

    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