本文整理汇总了Python中utils.counts函数的典型用法代码示例。如果您正苦于以下问题：Python counts函数的具体用法？Python counts怎么用？Python counts使用的例子？那么恭喜您, 这里精选的函数代码示例或许可以为您提供帮助。
在下文中一共展示了counts函数的15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_scale
def test_scale(self):
counts_left = utils.counts(utils.SEQUENCES_LEFT, 8)
counts_right = utils.counts(utils.SEQUENCES_RIGHT, 8)
filename_left = self.empty()
filename_right = self.empty()
with utils.open_profile(self.profile(counts_left, 8)) as handle_left:
with utils.open_profile(self.profile(counts_right, 8)) as handle_right:
with utils.open_profile(filename_left, 'w') as out_left:
with utils.open_profile(filename_right, 'w') as out_right:
kmer.scale(handle_left, handle_right, out_left, out_right)
if sum(counts_left.values()) < sum(counts_right.values()):
scale_left = sum(counts_right.values()) / sum(counts_left.values())
scale_right = 1.0
else:
scale_left = 1.0
scale_right = sum(counts_left.values()) / sum(counts_right.values())
for s in counts_left:
counts_left[s] *= scale_left
for s in counts_right:
counts_right[s] *= scale_right
utils.test_profile_file(filename_left, counts_left, 8)
utils.test_profile_file(filename_right, counts_right, 8)示例2: test_ProfileDistance_distance_k8
def test_ProfileDistance_distance_k8(self):
counts_a = utils.counts(utils.SEQUENCES_LEFT, 8)
counts_b = utils.counts(utils.SEQUENCES_RIGHT, 8)
profile_a = klib.Profile(utils.as_array(counts_a, 8))
profile_b = klib.Profile(utils.as_array(counts_b, 8))
k_dist = kdistlib.ProfileDistance()
np.testing.assert_almost_equal(k_dist.distance(profile_a, profile_b), 0.4626209322)示例3: test_profile_merge
def test_profile_merge(self):
counts_left = utils.counts(utils.SEQUENCES_LEFT, 8)
counts_right = utils.counts(utils.SEQUENCES_RIGHT, 8)
profile_left = klib.Profile(utils.as_array(counts_left, 8))
profile_right = klib.Profile(utils.as_array(counts_right, 8))
profile_left.merge(profile_right)
utils.test_profile(profile_left, counts_left + counts_right, 8)示例4: test_distance
def test_distance(self):
counts_left = utils.counts(utils.SEQUENCES_LEFT, 8)
counts_right = utils.counts(utils.SEQUENCES_RIGHT, 8)
out = StringIO()
with utils.open_profile(self.profile(counts_left, 8, 'left')) as handle_left:
with utils.open_profile(self.profile(counts_right, 8, 'right')) as handle_right:
kmer.distance(handle_left, handle_right, out)
assert out.getvalue() == 'left right %.10f\n' % 0.4626209323示例5: test_count_multi
def test_count_multi(self):
counts_left = utils.counts(utils.SEQUENCES_LEFT, 8)
counts_right = utils.counts(utils.SEQUENCES_RIGHT, 8)
filename = self.empty()
with open(self.fasta(utils.SEQUENCES_LEFT)) as handle_left:
with open(self.fasta(utils.SEQUENCES_RIGHT)) as handle_right:
with utils.open_profile(filename, 'w') as profile_handle:
kmer.count([handle_left, handle_right], profile_handle, 8, names=['a', 'b'])
utils.test_profile_file(filename, counts_left, 8, name='a')
utils.test_profile_file(filename, counts_right, 8, name='b')示例6: test_merge
def test_merge(self):
counts_left = utils.counts(utils.SEQUENCES_LEFT, 8)
counts_right = utils.counts(utils.SEQUENCES_RIGHT, 8)
filename = self.empty()
with utils.open_profile(self.profile(counts_left, 8)) as handle_left:
with utils.open_profile(self.profile(counts_right, 8)) as handle_right:
with utils.open_profile(filename, 'w') as profile_handle:
kmer.merge(handle_left, handle_right, profile_handle)
utils.test_profile_file(filename, counts_left + counts_right, 8)示例7: test_distance_smooth
def test_distance_smooth(self):
counts_left = utils.counts(utils.SEQUENCES_LEFT, 8)
counts_right = utils.counts(utils.SEQUENCES_RIGHT, 8)
out = StringIO()
with utils.open_profile(self.profile(counts_left, 8, 'left')) as handle_left:
with utils.open_profile(self.profile(counts_right, 8, 'right')) as handle_right:
kmer.distance(handle_left, handle_right, out, do_smooth=True, precision=3)
assert out.getvalue() == 'left right 0.077\n'示例8: test_distance_pairwise_expr
def test_distance_pairwise_expr(self):
counts_left = utils.counts(utils.SEQUENCES_LEFT, 8)
counts_right = utils.counts(utils.SEQUENCES_RIGHT, 8)
out = StringIO()
with utils.open_profile(self.profile(counts_left, 8, 'left')) as handle_left:
with utils.open_profile(self.profile(counts_right, 8, 'right')) as handle_right:
kmer.distance(handle_left, handle_right, out, precision=3,
custom_pairwise='abs(left - right) / (left + right + 1000)')
assert out.getvalue() == 'left right 0.001\n'示例9: test_distance_pairwise_name
def test_distance_pairwise_name(self):
counts_left = utils.counts(utils.SEQUENCES_LEFT, 8)
counts_right = utils.counts(utils.SEQUENCES_RIGHT, 8)
out = StringIO()
with utils.open_profile(self.profile(counts_left, 8, 'left')) as handle_left:
with utils.open_profile(self.profile(counts_right, 8, 'right')) as handle_right:
kmer.distance(handle_left, handle_right, out, precision=3,
custom_pairwise='numpy.multiply')
assert out.getvalue() == 'left right 0.084\n'示例10: test_cat_prefixes
def test_cat_prefixes(self):
counts_a = utils.counts(utils.SEQUENCES_LEFT, 8)
counts_b = utils.counts(utils.SEQUENCES_RIGHT, 8)
filename = self.empty()
with utils.open_profile(self.profile(counts_a, 8, name='X')) as handle_a:
with utils.open_profile(self.profile(counts_b, 8, name='X')) as handle_b:
with utils.open_profile(filename, 'w') as profile_handle:
kmer.cat([handle_a, handle_b], profile_handle, prefixes=['a_', 'b_'])
utils.test_profile_file(filename, counts_a, 8, name='a_X')
utils.test_profile_file(filename, counts_b, 8, name='b_X')示例11: test_distance_smooth_expr
def test_distance_smooth_expr(self):
counts_left = utils.counts(utils.SEQUENCES_LEFT, 8)
counts_right = utils.counts(utils.SEQUENCES_RIGHT, 8)
out = StringIO()
with utils.open_profile(self.profile(counts_left, 8, 'left')) as handle_left:
with utils.open_profile(self.profile(counts_right, 8, 'right')) as handle_right:
kmer.distance(handle_left, handle_right, out, do_smooth=True,
precision=3, custom_summary='np.max(values)')
assert out.getvalue() == 'left right 0.474\n'示例12: test_distance_matrix_two
def test_distance_matrix_two(self):
counts_left = utils.counts(utils.SEQUENCES_LEFT, 8)
counts_right = utils.counts(utils.SEQUENCES_RIGHT, 8)
profiles = [klib.Profile(utils.as_array(counts_left, 8), 'a'),
klib.Profile(utils.as_array(counts_right, 8), 'b')]
k_dist = kdistlib.ProfileDistance()
out = StringIO()
kdistlib.distance_matrix(profiles, out, 2, k_dist)
assert out.getvalue().strip().split('\n') == ['2', 'a', 'b', '0.46']示例13: test_ProfileDistance_distance_unmodified
def test_ProfileDistance_distance_unmodified(self):
counts_a = utils.counts(utils.SEQUENCES_LEFT, 8)
counts_b = utils.counts(utils.SEQUENCES_RIGHT, 8)
profile_a = klib.Profile(utils.as_array(counts_a, 8))
profile_b = klib.Profile(utils.as_array(counts_b, 8))
k_dist = kdistlib.ProfileDistance(do_balance=True)
k_dist.distance(profile_a, profile_b)
utils.test_profile(profile_a, counts_a, 8)
utils.test_profile(profile_b, counts_b, 8)示例14: test_distance_matrix_smooth
def test_distance_matrix_smooth(self):
counts_left = utils.counts(utils.SEQUENCES_LEFT, 8)
counts_right = utils.counts(utils.SEQUENCES_RIGHT, 8)
out = StringIO()
with utils.open_profile(self.multi_profile(8,
[counts_left,
counts_right,
counts_left],
['a', 'b', 'c'])) as handle:
kmer.distance_matrix(handle, out, do_smooth=True, precision=3)
assert out.getvalue().strip().split('\n') == ['3', 'a', 'b', 'c', '0.077', '0.000 0.077']示例15: test_count_multi_by_record
def test_count_multi_by_record(self):
counts_by_record_left = [utils.counts(record, 8) for record in utils.SEQUENCES_LEFT]
counts_by_record_right = [utils.counts(record, 8) for record in utils.SEQUENCES_RIGHT]
names_left = [str(i) for i, _ in enumerate(counts_by_record_left)]
names_right = [str(i) for i, _ in enumerate(counts_by_record_right)]
filename = self.empty()
with open(self.fasta(utils.SEQUENCES_LEFT, names=names_left)) as handle_left:
with open(self.fasta(utils.SEQUENCES_RIGHT, names=names_right)) as handle_right:
with utils.open_profile(filename, 'w') as profile_handle:
kmer.count([handle_left, handle_right], profile_handle, 8, names=['a', 'b'], by_record=True)
for name, counts in zip(names_left, counts_by_record_left):
utils.test_profile_file(filename, counts, 8, name='a_' + name)
for name, counts in zip(names_right, counts_by_record_right):
utils.test_profile_file(filename, counts, 8, name='b_' + name)