def test_sequence_collection_to_fastq_kwargs_passed(self):
for components, kwargs_expected_fp in self.valid_files:
for kwargs, expected_fp in kwargs_expected_fp:
obj = SequenceCollection([
NucleotideSequence(c[2], id=c[0], description=c[1],
quality=c[3]) for c in components])
fh = StringIO()
_sequence_collection_to_fastq(obj, fh, **kwargs)
observed = fh.getvalue()
fh.close()
with open(expected_fp, 'U') as f:
expected = f.read()
self.assertEqual(observed, expected)
def test_sequence_collection_to_fastq_kwargs_passed(self):
for components, kwargs_expected_fp in self.valid_files:
for kwargs, expected_fp in kwargs_expected_fp:
obj = SequenceCollection([
DNA(c[2], metadata={'id': c[0], 'description': c[1]},
positional_metadata={'quality': c[3]})
for c in components])
fh = StringIO()
_sequence_collection_to_fastq(obj, fh, **kwargs)
observed = fh.getvalue()
fh.close()
with open(expected_fp, 'U') as f:
expected = f.read()
self.assertEqual(observed, expected)
def test_sequence_collection_to_fastq_kwargs_passed(self):
for components, kwargs_expected_fp in self.valid_files:
for kwargs, expected_fp in kwargs_expected_fp:
obj = SequenceCollection([
NucleotideSequence(c[2],
id=c[0],
description=c[1],
quality=c[3]) for c in components
])
fh = StringIO()
_sequence_collection_to_fastq(obj, fh, **kwargs)
observed = fh.getvalue()
fh.close()
with open(expected_fp, 'U') as f:
expected = f.read()
self.assertEqual(observed, expected)
def test_sequence_collection_to_fastq_kwargs_passed(self):
for components, kwargs_expected_fp in self.valid_files:
for kwargs, expected_fp in kwargs_expected_fp:
obj = SequenceCollection([
DNA(c[2], metadata={'id': c[0], 'description': c[1]},
positional_metadata={'quality': c[3]},
lowercase='introns')
for c in components])
fh = StringIO()
kwargs['lowercase'] = 'introns'
_sequence_collection_to_fastq(obj, fh, **kwargs)
observed = fh.getvalue()
fh.close()
with open(expected_fp, 'U') as f:
expected = f.read()
self.assertEqual(observed, expected)