本文整理汇总了Python中khmer.GraphLabels.get_all_labels方法的典型用法代码示例。如果您正苦于以下问题：Python GraphLabels.get_all_labels方法的具体用法？Python GraphLabels.get_all_labels怎么用？Python GraphLabels.get_all_labels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.get_all_labels方法的3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_get_all_labels
# 需要导入模块: from khmer import GraphLabels [as 别名]
# 或者: from khmer.GraphLabels import get_all_labels [as 别名]
def test_get_all_labels():
lb = GraphLabels(20, 1e7, 4)
filename = utils.get_test_data('test-labels.fa')
lb.consume_seqfile_and_tag_with_labels(filename)
labels = lb.get_all_labels()
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示例2: test_get_labels_save_load
# 需要导入模块: from khmer import GraphLabels [as 别名]
# 或者: from khmer.GraphLabels import get_all_labels [as 别名]
def test_get_labels_save_load():
lb_pre = GraphLabels(20, 1e7, 4)
filename = utils.get_test_data('test-labels.fa')
lb_pre.consume_seqfile_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_all_labels()
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示例3: test_consume_seqfile_and_tag_with_labels
# 需要导入模块: from khmer import GraphLabels [as 别名]
# 或者: from khmer.GraphLabels import get_all_labels [as 别名]
def test_consume_seqfile_and_tag_with_labels():
lb = GraphLabels(20, 1e7, 4)
read_1 = 'ACGTAACCGGTTAAACCCGGGTTTAAAACCCCGGGGTTTT'
filename = utils.get_test_data('test-transcript.fa')
total_reads, _ = lb.consume_seqfile_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