def test_extract_reads_fail_identity(self):
with self.assertRaisesRegex(RuntimeError, "No matches found"):
extract_reads(self.sequences,
f_primer=self.f_primer,
r_primer=self.r_primer,
min_length=4,
identity=1)
def test_extract_reads_expected(self):
results = extract_reads(self.sequences,
f_primer=self.f_primer,
r_primer=self.r_primer,
min_length=4)
self._test_results(results)
def test_extract_reads_two_jobs(self):
results = extract_reads(self.sequences,
f_primer=self.f_primer,
r_primer=self.r_primer,
min_length=4,
n_jobs=2)
self._test_results(results)
def test_extract_reads_manual_batch_size(self):
results = extract_reads(self.sequences,
f_primer=self.f_primer,
r_primer=self.r_primer,
min_length=4,
batch_size=10)
self._test_results(results)
def test_extract_reads_expected_reverse(self):
reverse_sequences = Artifact.import_data(
'FeatureData[Sequence]',
self.get_data_path('dna-sequences-reverse.fasta'))
results = extract_reads(
reverse_sequences, f_primer=self.f_primer, r_primer=self.r_primer,
min_length=4, read_orientation='reverse')
self._test_results(results)
def test_extract_reads_expected_degenerate_primers(self):
degenerate_f_primer = 'WWWWW'
degenerate_r_primer = 'SSSSS'
degenerate_sequences = Artifact.import_data(
'FeatureData[Sequence]',
self.get_data_path('dna-sequences-degenerate-primers.fasta'))
results = extract_reads(
degenerate_sequences, f_primer=degenerate_f_primer,
r_primer=degenerate_r_primer, min_length=4)
self._test_results(results)
def test_extract_reads_expected_degenerate_primers(self):
degenerate_f_primer = 'WWWWW'
degenerate_r_primer = 'SSSSS'
degenerate_seqs = skbio.io.read(
self.get_data_path('dna-sequences-degenerate-primers.fasta'),
format='fasta',
constructor=skbio.DNA)
degenerate_tmp_seqs = os.path.join(self.temp_dir.name,
'degenerate-tmp-seqs.fasta')
skbio.io.write((s for s in degenerate_seqs), 'fasta',
degenerate_tmp_seqs)
degenerate_sequences = Artifact.import_data('FeatureData[Sequence]',
degenerate_tmp_seqs)
results = extract_reads(degenerate_sequences,
f_primer=degenerate_f_primer,
r_primer=degenerate_r_primer,
min_length=4)
self._test_results(results)
def test_extract_reads_fail_min_len_greater_than_trunc_len(self):
with self.assertRaisesRegex(ValueError, "minimum length setting"):
extract_reads(self.sequences,
f_primer=self.f_primer,
r_primer=self.r_primer,
trunc_len=1)
def test_extract_reads_fail_trim_entire_read(self):
with self.assertRaisesRegex(RuntimeError, "No matches found"):
extract_reads(self.sequences,
f_primer=self.f_primer,
r_primer=self.r_primer,
trim_left=4)
def test_extract_reads_expected_forward(self):
results = extract_reads(
self.sequences, f_primer=self.f_primer, r_primer=self.r_primer,
min_length=4, read_orientation='forward')
self._test_results(results)
