def test_invalid_lengths(self):
fh = StringIO("CLUSTAL\n"
"\n\n"
"abc GCAU\n"
"def -----\n")
with self.assertRaisesRegex(ClustalFormatError, r"not aligned"):
_clustal_to_tabular_msa(fh, constructor=CustomSequence)
def test_invalid_lengths(self):
fh = StringIO(
"CLUSTAL\n"
"\n\n"
"abc GCAU\n"
"def -----\n")
with self.assertRaisesRegex(ClustalFormatError, "not aligned"):
_clustal_to_tabular_msa(fh, constructor=CustomSequence)
def test_valid_tabular_msa_to_clustal_and_clustal_to_tabular_msa(self):
for valid_out in self.valid_clustal_out:
result_before = _clustal_to_tabular_msa(valid_out,
constructor=CustomSequence)
with StringIO() as fh:
_tabular_msa_to_clustal(result_before, fh)
fh.seek(0)
result_after = _clustal_to_tabular_msa(
fh, constructor=CustomSequence)
self.assertEqual(result_before, result_after)
def test_valid_tabular_msa_to_clustal_and_clustal_to_tabular_msa(self):
for valid_out in self.valid_clustal_out:
result_before = _clustal_to_tabular_msa(
valid_out, constructor=CustomSequence)
with StringIO() as fh:
_tabular_msa_to_clustal(result_before, fh)
fh.seek(0)
result_after = _clustal_to_tabular_msa(
fh, constructor=CustomSequence)
self.assertEqual(result_before, result_after)
def test_no_constructor(self):
with self.assertRaisesRegex(ValueError, r"`constructor`"):
_clustal_to_tabular_msa(self.valid_clustal_out[0])
def test_invalid_tabular_msa_to_clustal_and_clustal_to_tabular_msa(self):
for invalid_out in self.invalid_clustal_out:
with self.assertRaises(ClustalFormatError):
dict(
_clustal_to_tabular_msa(invalid_out,
constructor=CustomSequence))
def test_tabular_msa_to_clustal_with_bad_input(self):
BAD = StringIO('\n'.join(['dshfjsdfhdfsj', 'hfsdjksdfhjsdf']))
with self.assertRaises(ClustalFormatError):
dict(_clustal_to_tabular_msa(BAD, constructor=CustomSequence))
def test_tabular_msa_to_clustal_with_empty_input(self):
result = _clustal_to_tabular_msa(StringIO(),
constructor=CustomSequence)
self.assertEqual(dict(result), {})
def test_no_constructor(self):
with self.assertRaisesRegex(ValueError, "`constructor`"):
_clustal_to_tabular_msa(self.valid_clustal_out[0])
def test_invalid_tabular_msa_to_clustal_and_clustal_to_tabular_msa(self):
for invalid_out in self.invalid_clustal_out:
with self.assertRaises(ClustalFormatError):
dict(_clustal_to_tabular_msa(invalid_out,
constructor=CustomSequence))
def test_tabular_msa_to_clustal_with_bad_input(self):
BAD = StringIO('\n'.join(['dshfjsdfhdfsj', 'hfsdjksdfhjsdf']))
with self.assertRaises(ClustalFormatError):
dict(_clustal_to_tabular_msa(BAD, constructor=CustomSequence))
def test_tabular_msa_to_clustal_with_empty_input(self):
result = _clustal_to_tabular_msa(StringIO(),
constructor=CustomSequence)
self.assertEqual(dict(result), {})
