def test_fasta_to_tabular_msa(self):
test_cases = (self.empty, self.single,
self.tabular_msa_different_type,
self.lowercase_seqs)
# see comment in test_fasta_to_generator_valid_files (above) for
# testing strategy
for exp_list, kwargs, fasta_fps, qual_fps in test_cases:
if 'constructor' not in kwargs:
kwargs['constructor'] = CustomSequence
exp_list = [CustomSequence(seq) for seq in exp_list]
exp = TabularMSA(exp_list)
for fasta_fp in fasta_fps:
obs = _fasta_to_tabular_msa(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 = _fasta_to_tabular_msa(fasta_fp, qual=qual_fp,
**kwargs)
self.assertEqual(obs, exp)
def test_fasta_to_tabular_msa(self):
test_cases = (self.empty, self.single,
self.tabular_msa_different_type,
self.lowercase_seqs)
# see comment in test_fasta_to_generator_valid_files (above) for
# testing strategy
for exp_list, kwargs, fasta_fps, qual_fps in test_cases:
if 'constructor' not in kwargs:
kwargs['constructor'] = CustomSequence
exp_list = [CustomSequence(seq) for seq in exp_list]
exp = TabularMSA(exp_list)
for fasta_fp in fasta_fps:
obs = _fasta_to_tabular_msa(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 = _fasta_to_tabular_msa(fasta_fp, qual=qual_fp,
**kwargs)
self.assertEqual(obs, exp)
def test_fasta_to_tabular_msa_no_constructor(self):
with self.assertRaisesRegex(ValueError, '`constructor`'):
_fasta_to_tabular_msa(get_data_path('fasta_single_seq'))
def test_fasta_to_tabular_msa_no_constructor(self):
with six.assertRaisesRegex(self, ValueError, '`constructor`'):
_fasta_to_tabular_msa(get_data_path('fasta_single_seq'))
