def test_generator_to_fastq_no_qual(self):
def gen():
yield BiologicalSequence('ACGT', id='foo', description='bar',
quality=range(4))
yield BiologicalSequence('ACG', id='foo', description='bar')
with self.assertRaisesRegexp(ValueError, '2nd.*quality scores'):
_generator_to_fastq(gen(), StringIO(), variant='illumina1.8')
def test_generator_to_fastq_no_qual(self):
def gen():
yield Sequence('ACGT',
metadata={'id': 'foo', 'description': 'bar'},
positional_metadata={'quality': range(4)})
yield Sequence('ACG', metadata={'id': 'foo', 'description': 'bar'})
with self.assertRaisesRegexp(ValueError, '2nd.*quality scores'):
_generator_to_fastq(gen(), StringIO(), variant='illumina1.8')
def test_generator_to_fastq_no_qual(self):
def gen():
yield Sequence('ACGT',
metadata={'id': 'foo', 'description': 'bar'},
positional_metadata={'quality': range(4)})
yield Sequence('ACG', metadata={'id': 'foo', 'description': 'bar'})
with six.assertRaisesRegex(self, ValueError, '2nd.*quality scores'):
_generator_to_fastq(gen(), StringIO(), variant='illumina1.8')
def test_generator_to_fastq_no_qual(self):
def gen():
yield BiologicalSequence('ACGT',
id='foo',
description='bar',
quality=range(4))
yield BiologicalSequence('ACG', id='foo', description='bar')
with self.assertRaisesRegexp(ValueError, '2nd.*quality scores'):
_generator_to_fastq(gen(), StringIO(), variant='illumina1.8')
def test_conversion(self):
for from_fp, to_fp, kwargs in self.conversions:
for from_kwargs, to_kwargs in kwargs:
read_gen = _fastq_to_generator(from_fp, **from_kwargs)
fh = StringIO()
# will issue warning when truncating quality scores
with warnings.catch_warnings(record=True):
warnings.simplefilter("ignore")
_generator_to_fastq(read_gen, fh, **to_kwargs)
obs = fh.getvalue()
fh.close()
with open(to_fp, 'U') as fh:
exp = fh.read()
self.assertEqual(obs, exp)
def test_conversion(self):
for from_fp, to_fp, kwargs in self.conversions:
for from_kwargs, to_kwargs in kwargs:
read_gen = _fastq_to_generator(from_fp, **from_kwargs)
fh = StringIO()
# will issue warning when truncating quality scores
with warnings.catch_warnings(record=True):
warnings.simplefilter("ignore")
_generator_to_fastq(read_gen, fh, **to_kwargs)
obs = fh.getvalue()
fh.close()
with open(to_fp, 'U') as fh:
exp = fh.read()
self.assertEqual(obs, exp)
def test_generator_to_fastq_kwargs_passed(self):
for components, kwargs_expected_fp in self.valid_files:
for kwargs, expected_fp in kwargs_expected_fp:
def gen():
for c in components:
yield BiologicalSequence(
c[2], id=c[0], description=c[1], quality=c[3])
fh = StringIO()
_generator_to_fastq(gen(), fh, **kwargs)
observed = fh.getvalue()
fh.close()
with open(expected_fp, 'U') as f:
expected = f.read()
self.assertEqual(observed, expected)
def test_generator_to_fastq_kwargs_passed(self):
for components, kwargs_expected_fp in self.valid_files:
for kwargs, expected_fp in kwargs_expected_fp:
def gen():
for c in components:
yield Sequence(
c[2], metadata={'id': c[0], 'description': c[1]},
positional_metadata={'quality': c[3]})
fh = StringIO()
_generator_to_fastq(gen(), fh, **kwargs)
observed = fh.getvalue()
fh.close()
with open(expected_fp, 'U') as f:
expected = f.read()
self.assertEqual(observed, expected)
def test_generator_to_fastq_kwargs_passed(self):
for components, kwargs_expected_fp in self.valid_files:
for kwargs, expected_fp in kwargs_expected_fp:
def gen():
for c in components:
yield Sequence(
c[2], metadata={'id': c[0], 'description': c[1]},
positional_metadata={'quality': c[3]})
fh = StringIO()
_generator_to_fastq(gen(), fh, **kwargs)
observed = fh.getvalue()
fh.close()
with open(expected_fp, 'U') as f:
expected = f.read()
self.assertEqual(observed, expected)
def test_generator_to_fastq_kwargs_passed(self):
for components, kwargs_expected_fp in self.valid_files:
for kwargs, expected_fp in kwargs_expected_fp:
def gen():
for c in components:
yield BiologicalSequence(c[2],
id=c[0],
description=c[1],
quality=c[3])
fh = StringIO()
_generator_to_fastq(gen(), fh, **kwargs)
observed = fh.getvalue()
fh.close()
with open(expected_fp, 'U') as f:
expected = f.read()
self.assertEqual(observed, expected)