def test_valid_alignment_to_clustal_and_clustal_to_alignment(self):
for valid_out in self.valid_clustal_out:
result_before = _clustal_to_alignment(valid_out)
with StringIO() as fh:
_alignment_to_clustal(result_before, fh)
fh.seek(0)
result_after = _clustal_to_alignment(fh)
self.assertEqual(result_before, result_after)
def test_alignment_to_clustal_with_bad_input(self):
BAD = StringIO(u'\n'.join(['dshfjsdfhdfsj', 'hfsdjksdfhjsdf']))
result = _clustal_to_alignment(BAD, strict=False)
self.assertEqual(dict(result), {})
# should fail unless we turned strict processing off
with self.assertRaises(ClustalFormatError):
BAD.seek(0)
dict(_clustal_to_alignment(BAD))
def test_invalid_alignment_to_clustal_and_clustal_to_alignment(self):
for invalid_out in self.invalid_clustal_out:
with self.assertRaises(ClustalFormatError):
dict(_clustal_to_alignment(invalid_out, strict=True))
def test_alignment_to_clustal_with_empty_input(self):
result = _clustal_to_alignment(StringIO())
self.assertEqual(dict(result), {})
def test_alignment_to_clustal_with_empty_input(self):
result = _clustal_to_alignment(StringIO())
self.assertEqual(dict(result), {})
