def test_count(self):
counts = utils.counts(utils.SEQUENCES, 8)
filename = self.empty()
with open(self.fasta(utils.SEQUENCES)) as fasta_handle:
with utils.open_profile(filename, 'w') as profile_handle:
kmer.count([fasta_handle], profile_handle, 8)
utils.test_profile_file(filename, counts, 8)
def test_count(self):
counts = utils.counts(utils.SEQUENCES, 8)
filename = self.empty()
with open(self.fasta(utils.SEQUENCES)) as fasta_handle:
with utils.open_profile(filename, 'w') as profile_handle:
kmer.count([fasta_handle], profile_handle, 8)
utils.test_profile_file(filename, counts, 8)
def test_count_by_record(self):
counts_by_record = [utils.counts(record, 8) for record in utils.SEQUENCES]
names = [str(i) for i, _ in enumerate(counts_by_record)]
filename = self.empty()
with open(self.fasta(utils.SEQUENCES, names=names)) as fasta_handle:
with utils.open_profile(filename, 'w') as profile_handle:
kmer.count([fasta_handle], profile_handle, 8, by_record=True)
for name, counts in zip(names, counts_by_record):
utils.test_profile_file(filename, counts, 8, name=name)
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')
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)
