def test_phylip_to_alignment_valid_files(self):
for valid_files, components in self.valid_configurations:
for valid in valid_files:
observed = _phylip_to_alignment(valid)
expected = Alignment([Sequence(seq, metadata={'id': ID})
for (seq, ID) in components])
self.assertEqual(observed, expected)
def test_phylip_to_alignment_valid_files(self):
for valid_files, components in self.valid_configurations:
for valid in valid_files:
observed = _phylip_to_alignment(valid)
expected = Alignment([
Sequence(seq, metadata={'id': ID})
for (seq, ID) in components
])
self.assertEqual(observed, expected)
def test_phylip_to_alignment_invalid_files(self):
# files that should be invalid for all variants, as well as custom
# phred offsets
for fp, error_type, error_msg_regex in self.invalid_files:
with six.assertRaisesRegex(self, error_type, error_msg_regex):
_phylip_to_alignment(fp)
def test_phylip_to_alignment_invalid_files(self):
# files that should be invalid for all variants, as well as custom
# phred offsets
for fp, error_type, error_msg_regex in self.invalid_files:
with six.assertRaisesRegex(self, error_type, error_msg_regex):
_phylip_to_alignment(fp)
