def test_roundtrip_generators(self):
# test that fasta and qual files can be streamed into memory and back
# out to disk using generator reader and writer
fps = list(map(lambda e: list(map(get_data_path, e)),
[('empty', 'empty'),
('fasta_multi_seq_roundtrip',
'qual_multi_seq_roundtrip')]))
for fasta_fp, qual_fp in fps:
with open(fasta_fp, 'U') as fh:
exp_fasta = fh.read()
with open(qual_fp, 'U') as fh:
exp_qual = fh.read()
fasta_fh = StringIO()
qual_fh = StringIO()
_generator_to_fasta(_fasta_to_generator(fasta_fp, qual=qual_fp),
fasta_fh, qual=qual_fh)
obs_fasta = fasta_fh.getvalue()
obs_qual = qual_fh.getvalue()
fasta_fh.close()
qual_fh.close()
self.assertEqual(obs_fasta, exp_fasta)
self.assertEqual(obs_qual, exp_qual)
def test_generator_to_fasta_sequence_lowercase_exception(self):
seq = Sequence('ACgt', metadata={'id': ''})
fh = StringIO()
with self.assertRaisesRegexp(AttributeError,
"lowercase specified but class Sequence "
"does not support lowercase "
"functionality"):
_generator_to_fasta(SequenceCollection([seq]), fh,
lowercase='introns')
def test_generator_to_fasta_no_qual(self):
# test writing standalone fasta (i.e., without a qual file)
for obj, kwargs, fp, _ in self.objs_fps:
fh = StringIO()
_generator_to_fasta(obj, fh, **kwargs)
obs = fh.getvalue()
fh.close()
with open(fp, 'U') as fh:
exp = fh.read()
self.assertEqual(obs, exp)
def test_generator_to_fasta(self):
for obj, kwargs, fp in self.objs_fps:
fh = StringIO()
_generator_to_fasta(obj, fh, **kwargs)
obs = fh.getvalue()
fh.close()
with open(fp, 'U') as fh:
exp = fh.read()
self.assertEqual(obs, exp)
def test_generator_to_fasta_mixed_qual_scores(self):
# test writing some sequences with qual scores and some without is
# possible if no qual output file is specified
fh = StringIO()
_generator_to_fasta(self.mixed_qual_score_gen, fh, lowercase='introns')
obs = fh.getvalue()
fh.close()
with open(get_data_path('fasta_mixed_qual_scores'), 'U') as fh:
exp = fh.read()
self.assertEqual(obs, exp)
def test_roundtrip_generators(self):
# test that a file can be streamed into memory and back out to disk
# using generator reader and writer
for fp in map(get_data_path, ['empty', 'fasta_multi_seq_roundtrip']):
with open(fp, 'U') as fh:
exp = fh.read()
fh = StringIO()
_generator_to_fasta(_fasta_to_generator(fp), fh)
obs = fh.getvalue()
fh.close()
self.assertEqual(obs, exp)
def test_generator_to_fasta_with_qual(self):
# test writing fasta and qual files
for obj, kwargs, fasta_fp, qual_fp in self.objs_fps:
if qual_fp is not None:
fasta_fh = StringIO()
qual_fh = StringIO()
_generator_to_fasta(obj, fasta_fh, qual=qual_fh, **kwargs)
obs_fasta = fasta_fh.getvalue()
obs_qual = qual_fh.getvalue()
fasta_fh.close()
qual_fh.close()
with open(fasta_fp, 'U') as fh:
exp_fasta = fh.read()
with open(qual_fp, 'U') as fh:
exp_qual = fh.read()
self.assertEqual(obs_fasta, exp_fasta)
self.assertEqual(obs_qual, exp_qual)
def test_generator_to_fasta_invalid_input(self):
for obj, kwargs, error_type, error_msg_regexp in self.invalid_objs:
fh = StringIO()
with self.assertRaisesRegexp(error_type, error_msg_regexp):
_generator_to_fasta(obj, fh, **kwargs)
fh.close()