本文整理汇总了Python中khmer.LabelHash.sweep_tag_neighborhood方法的典型用法代码示例。如果您正苦于以下问题：Python LabelHash.sweep_tag_neighborhood方法的具体用法？Python LabelHash.sweep_tag_neighborhood怎么用？Python LabelHash.sweep_tag_neighborhood使用的例子？那么恭喜您, 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.LabelHash的用法示例。
在下文中一共展示了LabelHash.sweep_tag_neighborhood方法的4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 LabelHash [as 别名]
# 或者: from khmer.LabelHash import sweep_tag_neighborhood [as 别名]
def test_label_tag_correctness_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)
# 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_tag_neighborhood
# 需要导入模块: from khmer import LabelHash [as 别名]
# 或者: from khmer.LabelHash import sweep_tag_neighborhood [as 别名]
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示例3: test_label_tag_correctness
# 需要导入模块: from khmer import LabelHash [as 别名]
# 或者: from khmer.LabelHash import sweep_tag_neighborhood [as 别名]
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示例4: test_consume_fasta_and_tag_with_labels
# 需要导入模块: from khmer import LabelHash [as 别名]
# 或者: from khmer.LabelHash import sweep_tag_neighborhood [as 别名]
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.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.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