def test_profile_from_file(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)
utils.test_profile(profile, counts, 4)
def test_profile_balance(self):
counts = utils.counts(utils.SEQUENCES, 8)
profile = klib.Profile(utils.as_array(counts, 8))
profile.balance()
counts.update(
dict((utils.reverse_complement(s), c) for s, c in counts.items()))
utils.test_profile(profile, counts, 8)
def test_profile_balance_palindrome(self):
counts = utils.counts(['AATT'], 4)
profile = klib.Profile(utils.as_array(counts, 4))
profile.balance()
counts.update(
dict((utils.reverse_complement(s), c) for s, c in counts.items()))
utils.test_profile(profile, counts, 4)
def _test_from_fasta_by_record(self, sequences, k, prefix=None):
counts_by_record = [utils.counts(sequence, k) for sequence in sequences]
names = [str(i) for i, _ in enumerate(counts_by_record)]
with open(self.fasta(sequences, names=names)) as fasta_handle:
profiles = klib.Profile.from_fasta_by_record(fasta_handle, k, prefix=prefix)
for name, counts, profile in zip(names, counts_by_record, profiles):
prefixed_name = prefix + '_' + name if prefix else name
utils.test_profile(profile, counts, k, name=prefixed_name)
def test_profile_balance_palindrome(self):
counts = utils.counts(['AATT'], 4)
profile = klib.Profile(utils.as_array(counts, 4))
profile.balance()
counts.update(dict((utils.reverse_complement(s), c)
for s, c in counts.items()))
utils.test_profile(profile, counts, 4)
def test_profile_balance(self):
counts = utils.counts(utils.SEQUENCES, 8)
profile = klib.Profile(utils.as_array(counts, 8))
profile.balance()
counts.update(dict((utils.reverse_complement(s), c)
for s, c in counts.items()))
utils.test_profile(profile, counts, 8)
def test_profile_shrink_max(self):
counts = utils.counts(utils.SEQUENCES, 4)
profile = klib.Profile(utils.as_array(counts, 4))
profile.shrink(3)
counts = Counter(
dict((t, sum(counts[u] for u in counts if u.startswith(t)))
for t in set(s[:-3] for s in counts)))
utils.test_profile(profile, counts, 1)
def test_profile_shrink_max(self):
counts = utils.counts(utils.SEQUENCES, 4)
profile = klib.Profile(utils.as_array(counts, 4))
profile.shrink(3)
counts = Counter(dict((t, sum(counts[u] for u in counts
if u.startswith(t)))
for t in set(s[:-3] for s in counts)))
utils.test_profile(profile, counts, 1)
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)
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)
def test_profile_shuffle(self):
counts = utils.counts(utils.SEQUENCES, 2)
profile = klib.Profile(utils.as_array(counts, 2))
np.random.seed(100)
profile.shuffle()
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(profile, counts, 2)
def test_profile_shuffle(self):
counts = utils.counts(utils.SEQUENCES, 2)
profile = klib.Profile(utils.as_array(counts, 2))
np.random.seed(100)
profile.shuffle()
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(profile, counts, 2)
def test_profile_save_from_file(self):
counts = utils.counts(utils.SEQUENCES, 4)
profile = klib.Profile(utils.as_array(counts, 4))
filename = self.empty()
with utils.open_profile(filename, 'w') as profile_handle:
profile.save(profile_handle)
with utils.open_profile(filename, 'r') as profile_handle:
profile = klib.Profile.from_file(profile_handle)
utils.test_profile(profile, counts, 4)
def test_profile_save_from_file(self):
counts = utils.counts(utils.SEQUENCES, 4)
profile = klib.Profile(utils.as_array(counts, 4))
filename = self.empty()
with utils.open_profile(filename, 'w') as profile_handle:
profile.save(profile_handle)
with utils.open_profile(filename, 'r') as profile_handle:
profile = klib.Profile.from_file(profile_handle)
utils.test_profile(profile, counts, 4)
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)
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)
def _test_from_fasta_by_record(self, sequences, k, prefix=None):
counts_by_record = [
utils.counts(sequence, k) for sequence in sequences
]
names = [str(i) for i, _ in enumerate(counts_by_record)]
with open(self.fasta(sequences, names=names)) as fasta_handle:
profiles = klib.Profile.from_fasta_by_record(fasta_handle,
k,
prefix=prefix)
for name, counts, profile in zip(names, counts_by_record,
profiles):
prefixed_name = prefix + '_' + name if prefix else name
utils.test_profile(profile, counts, k, name=prefixed_name)
def test_profile_from_file_old_format(self):
counts = utils.counts(utils.SEQUENCES, 4)
with open(self.profile_old_format(counts, 4)) as handle:
profile = klib.Profile.from_file_old_format(handle)
utils.test_profile(profile, counts, 4)
def _test_from_fasta(self, sequences, k, name=None):
counts = utils.counts(sequences, k)
with open(self.fasta(sequences)) as fasta_handle:
profile = klib.Profile.from_fasta(fasta_handle, k, name=name)
utils.test_profile(profile, counts, k, name=name)
def test_profile(self):
counts = utils.counts(utils.SEQUENCES, 8)
profile = klib.Profile(utils.as_array(counts, 8))
utils.test_profile(profile, counts, 8)
def _test_from_fasta(self, sequences, k, name=None):
counts = utils.counts(sequences, k)
with open(self.fasta(sequences)) as fasta_handle:
profile = klib.Profile.from_fasta(fasta_handle, k, name=name)
utils.test_profile(profile, counts, k, name=name)
def test_profile(self):
counts = utils.counts(utils.SEQUENCES, 8)
profile = klib.Profile(utils.as_array(counts, 8))
utils.test_profile(profile, counts, 8)
def test_profile_from_file_old_format(self):
counts = utils.counts(utils.SEQUENCES, 4)
with open(self.profile_old_format(counts, 4)) as handle:
profile = klib.Profile.from_file_old_format(handle)
utils.test_profile(profile, counts, 4)
def test_profile_from_file(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)
utils.test_profile(profile, counts, 4)