def test_strict_interleaved_dna_valid_chars_clean_str(self):
pr = phylip.PhylipReader(data_type='dna',
strict=True,
interleaved=True,
multispace_delimiter=False,
underscores_to_spaces=False,
ignore_invalid_chars=False)
dataset = pr.read(
StringIO(strict_interleaved_dna_valid_chars_clean_str))
self.verify(dataset)
def test_raises_error_strict_sequential_dna_invalid_chars_messy_str(self):
pr = phylip.PhylipReader(data_type='dna',
strict=True,
interleaved=False,
multispace_delimiter=False,
underscores_to_spaces=False,
ignore_invalid_chars=False)
self.assertRaises(
phylip.PhylipReader.PhylipStrictSequentialError, pr.read,
StringIO(strict_sequential_dna_invalid_chars_messy_str))
def test_relaxed_multi_space_dna_valid_chars_clean_str(self):
pr = phylip.PhylipReader(data_type='dna',
strict=False,
interleaved=True,
multispace_delimiter=True,
underscores_to_spaces=True,
ignore_invalid_chars=False)
s = relaxed_interleaved_dna_valid_chars_clean_str.replace(
'$', ' ').replace('_', ' ')
dataset = pr.read(StringIO(s))
self.verify(dataset, underscores_to_spaces=True)
def test_relaxed_single_space_dna_invalid_chars_messy_str_no_underscores(
self):
pr = phylip.PhylipReader(data_type='dna',
strict=False,
interleaved=False,
multispace_delimiter=False,
underscores_to_spaces=True,
ignore_invalid_chars=True)
s = relaxed_sequential_dna_invalid_chars_messy_str.replace('$', ' ')
dataset = pr.read(StringIO(s))
self.verify(dataset, underscores_to_spaces=True)
