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
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
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
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
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, _ = 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 all labels")
print(lb.get_all_labels())
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
def test_consume_partitioned_fasta_and_tag_with_labels():
lb = GraphLabels(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
