def test_fasta_to_generator_valid_files(self):
test_cases = (self.empty, self.single, self.multi,
self.odd_labels_different_type,
self.sequence_collection_different_type,
self.lowercase_seqs)
# Strategy:
# for each fasta file, read it without its corresponding qual file,
# and ensure observed vs. expected match, ignoring quality scores in
# expected. next, parse the current fasta file with each
# corresponding quality file and ensure that observed vs. expected
# match, this time taking quality scores into account. this
# sufficiently exercises parsing a standalone fasta file and paired
# fasta/qual files
for exp, kwargs, fasta_fps, qual_fps in test_cases:
for fasta_fp in fasta_fps:
obs = list(_fasta_to_generator(fasta_fp, **kwargs))
self.assertEqual(len(obs), len(exp))
for o, e in zip(obs, exp):
e = e.copy()
del e.positional_metadata['quality']
self.assertEqual(o, e)
for qual_fp in qual_fps:
obs = list(_fasta_to_generator(fasta_fp, qual=qual_fp,
**kwargs))
self.assertEqual(len(obs), len(exp))
for o, e in zip(obs, exp):
self.assertEqual(o, e)
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_fasta_to_generator_valid_files(self):
for exp, kwargs, fps in (self.empty, self.single, self.multi,
self.odd_labels_different_type,
self.sequence_collection_different_type):
for fp in fps:
obs = list(_fasta_to_generator(fp, **kwargs))
self.assertEqual(len(obs), len(exp))
for o, e in zip(obs, exp):
self.assertTrue(o.equals(e))
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_fasta_to_generator_invalid_files(self):
for fp, kwargs, error_type, error_msg_regex in self.invalid_fps:
with self.assertRaisesRegexp(error_type, error_msg_regex):
list(_fasta_to_generator(fp, **kwargs))
def test_fasta_to_generator_invalid_files(self):
for fp, error_msg_regex in self.invalid_fps:
with self.assertRaisesRegexp(FASTAFormatError, error_msg_regex):
list(_fasta_to_generator(fp))