def test_phylip_to_tabular_msa_valid_files(self):
for valid_files, components in self.valid_configurations:
for valid in valid_files:
observed = _phylip_to_tabular_msa(valid, constructor=DNA)
expected_seqs = []
expected_index = []
for seq, ID in components:
expected_seqs.append(DNA(seq))
expected_index.append(ID)
expected = TabularMSA(expected_seqs, index=expected_index)
self.assertEqual(observed, expected)
def test_phylip_to_tabular_msa_valid_files(self):
for valid_files, components in self.valid_configurations:
for valid in valid_files:
observed = _phylip_to_tabular_msa(valid, constructor=DNA)
expected_seqs = []
expected_index = []
for seq, ID in components:
expected_seqs.append(DNA(seq))
expected_index.append(ID)
expected = TabularMSA(expected_seqs, index=expected_index)
self.assertEqual(observed, expected)
def test_phylip_to_tabular_msa_no_constructor(self):
with self.assertRaisesRegex(ValueError, '`constructor`'):
_phylip_to_tabular_msa(get_data_path('phylip_dna_3_seqs'))
def test_phylip_to_tabular_msa_invalid_files(self):
for fp, error_type, error_msg_regex in self.invalid_files:
with self.assertRaisesRegex(error_type, error_msg_regex):
_phylip_to_tabular_msa(fp, constructor=DNA)
def test_phylip_to_tabular_msa_no_constructor(self):
with six.assertRaisesRegex(self, ValueError, '`constructor`'):
_phylip_to_tabular_msa(get_data_path('phylip_dna_3_seqs'))
def test_phylip_to_tabular_msa_invalid_files(self):
for fp, error_type, error_msg_regex in self.invalid_files:
with six.assertRaisesRegex(self, error_type, error_msg_regex):
_phylip_to_tabular_msa(fp, constructor=DNA)