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)