本文整理汇总了Python中khmer.GraphLabels.sweep_label_neighborhood方法的典型用法代码示例。如果您正苦于以下问题：Python GraphLabels.sweep_label_neighborhood方法的具体用法？Python GraphLabels.sweep_label_neighborhood怎么用？Python GraphLabels.sweep_label_neighborhood使用的例子？那么, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类khmer.GraphLabels的用法示例。
在下文中一共展示了GraphLabels.sweep_label_neighborhood方法的6个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: test_label_tag_correctness_save_load
# 需要导入模块: from khmer import GraphLabels [as 别名]
# 或者: from khmer.GraphLabels import sweep_label_neighborhood [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示例2: test_sweep_label_neighborhood
# 需要导入模块: from khmer import GraphLabels [as 别名]
# 或者: from khmer.GraphLabels import sweep_label_neighborhood [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示例3: test_label_tag_correctness
# 需要导入模块: from khmer import GraphLabels [as 别名]
# 或者: from khmer.GraphLabels import sweep_label_neighborhood [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示例4: test_consume_sequence_and_tag_with_labels
# 需要导入模块: from khmer import GraphLabels [as 别名]
# 或者: from khmer.GraphLabels import sweep_label_neighborhood [as 别名]
def test_consume_sequence_and_tag_with_labels():
lb = GraphLabels(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示例5: test_consume_partitioned_fasta_and_tag_with_labels
# 需要导入模块: from khmer import GraphLabels [as 别名]
# 或者: from khmer.GraphLabels import sweep_label_neighborhood [as 别名]
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示例6: test_consume_fasta_and_tag_with_labels
# 需要导入模块: from khmer import GraphLabels [as 别名]
# 或者: from khmer.GraphLabels import sweep_label_neighborhood [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