本文整理汇总了Python中utils.open_profile函数的典型用法代码示例。如果您正苦于以下问题：Python open_profile函数的具体用法？Python open_profile怎么用？Python open_profile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open_profile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_balance
def test_balance(self):
counts = utils.counts(utils.SEQUENCES, 8)
filename = self.empty()
with utils.open_profile(self.profile(counts, 8)) as input_handle:
with utils.open_profile(filename, 'w') as output_handle:
kmer.balance(input_handle, output_handle)
counts.update(dict((utils.reverse_complement(s), c) for s, c in counts.items()))
utils.test_profile_file(filename, counts, 8)示例3: test_profile_from_file_save
def test_profile_from_file_save(self):
counts = utils.counts(utils.SEQUENCES, 4)
with utils.open_profile(self.profile(counts, 4), 'r') as profile_handle:
profile = klib.Profile.from_file(profile_handle)
filename = self.empty()
with utils.open_profile(filename, 'w') as profile_handle:
profile.save(profile_handle)
utils.test_profile_file(filename, counts, 4)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_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_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_shrink
def test_shrink(self):
counts = utils.counts(utils.SEQUENCES, 8)
filename = self.empty()
with utils.open_profile(self.profile(counts, 8)) as input_handle:
with utils.open_profile(filename, 'w') as output_handle:
kmer.shrink(input_handle, output_handle, 1)
counts = Counter(dict((t, sum(counts[u] for u in counts
if u.startswith(t)))
for t in set(s[:-1] for s in counts)))
utils.test_profile_file(filename, counts, 7)示例12: test_smooth_custom_name
def test_smooth_custom_name(self):
# See test_kdistlib.test_ProfileDistance_dynamic_smooth
counts_left = Counter(['AC', 'AG', 'AT', 'CA', 'CC', 'CG', 'CT', 'GA', 'GC', 'GG', 'GT', 'TA', 'TG', 'TT'])
counts_right = Counter(['AC', 'AT', 'CA', 'CC', 'CG', 'CT', 'GA', 'GC', 'GG', 'GT', 'TA', 'TC', 'TG', 'TT'])
filename_left = self.empty()
filename_right = self.empty()
with utils.open_profile(self.profile(counts_left, 2)) as handle_left:
with utils.open_profile(self.profile(counts_right, 2)) as handle_right:
with utils.open_profile(filename_left, 'w') as out_left:
with utils.open_profile(filename_right, 'w') as out_right:
kmer.smooth(handle_left, handle_right, out_left, out_right, custom_summary='numpy.max')示例13: test_shuffle
def test_shuffle(self):
# See test_klib.profile_shuffle
counts = utils.counts(utils.SEQUENCES, 2)
filename = self.empty()
with utils.open_profile(self.profile(counts, 2)) as input_handle:
with utils.open_profile(filename, 'w') as output_handle:
np.random.seed(100)
kmer.shuffle(input_handle, output_handle)
counts = dict(zip([''.join(s) for s in itertools.product('ACGT', repeat=2)],
[13, 7, 6, 18, 12, 1, 13, 17, 16, 12, 23, 27, 24, 17, 18, 12]))
utils.test_profile_file(filename, counts, 2)示例14: test_merge_custom_name
def test_merge_custom_name(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, custom_merger='numpy.multiply')
counts_mult = Counter(dict((s, counts_left[s] * counts_right[s])
for s in set(counts_left) & set(counts_right)))
utils.test_profile_file(filename, counts_mult, 8)示例15: test_merge_custom_expr
def test_merge_custom_expr(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, custom_merger='(left + right) * np.logical_xor(left, right)')
counts_xor = counts_left + counts_right
for s in set(counts_left) & set(counts_right):
del counts_xor[s]
utils.test_profile_file(filename, counts_xor, 8)