def test_letter_code_not_str(self):
with pytest.raises(TypeError):
LetterCode(1)
with pytest.raises(TypeError):
LetterCode([])
with pytest.raises(TypeError):
LetterCode(LetterCode('A'))
def test_letter_type_incorrect(self):
with pytest.raises(TypeError):
LetterCode('A', 1)
with pytest.raises(TypeError):
LetterCode('A', [])
with pytest.raises(TypeError):
LetterCode('A', '')
with pytest.raises(TypeError):
LetterCode('A', 'aminoacidnucleotide')
def test_letter_code_lower_case(self):
letter_code = LetterCode('a', 'nucleotide')
assert letter_code.letter_code == 'A'
assert letter_code.letter_type == 'nucleotide'
assert letter_code.description == 'adenosine'
assert letter_code.degenerate is False
assert letter_code.supported is True
assert letter_code.in_fasta_spec is True
def test_lettercode_good(self, nucleotide_good):
new = LetterCode.from_lettercode(nucleotide_good)
assert new is not nucleotide_good
assert new.letter_code == nucleotide_good.letter_code
assert new.letter_type == nucleotide_good.letter_type
assert new.description == nucleotide_good.description
assert new.degenerate == nucleotide_good.degenerate
assert new.supported == nucleotide_good.supported
assert new.in_fasta_spec == nucleotide_good.in_fasta_spec
def test_letter_type_none(self, letter_type_none):
with pytest.warns(UserWarning):
complement = letter_type_none.complement()
assert complement.letter_code == 'T'
assert complement.letter_type is None
assert complement.description == ''
assert complement.degenerate is None
assert complement.supported is False
assert complement.in_fasta_spec is True
# aminoacid letter code that is not also a nucleotide
with pytest.warns(UserWarning):
aminoacid = LetterCode('X').complement()
assert aminoacid.letter_code == 'X'
assert aminoacid.letter_type is None
assert aminoacid.description == ''
assert aminoacid.degenerate is None
assert aminoacid.supported is False
assert aminoacid.in_fasta_spec is True
def letter_codes_unknown(unknown_characters):
letter_codes = [LetterCode(character) for character in unknown_characters]
return zip(letter_codes, unknown_characters)
def letter_type_none():
return LetterCode('A')
def test_lettercode(self, nucleotide_good):
assert nucleotide_good == LetterCode('A')
assert nucleotide_good.__eq__(LetterCode('A'))
assert not nucleotide_good == LetterCode('C')
def aminoacid_degenerate():
return LetterCode('-', 'aminoacid')
def aminoacid_good():
return LetterCode('H', 'aminoacid')
def test_letter_code_multiple_characters(self):
with pytest.raises(TypeError):
LetterCode('AC')
def test_lettercode_wrong_type(self):
with pytest.raises(TypeError):
LetterCode.from_lettercode('A')
with pytest.raises(TypeError):
LetterCode.from_lettercode(1)
def nucleotide_good():
return LetterCode('A', 'nucleotide')
def test_letter_code_empty_str(self):
with pytest.raises(TypeError):
LetterCode('')
def letter_codes_unknown_nucleotide(unknown_characters):
letter_codes = [
LetterCode(character, 'nucleotide') for character in unknown_characters
]
return zip(letter_codes, unknown_characters)
def letter_codes_unknown_aminoacid(unknown_characters):
letter_codes = [
LetterCode(character, 'aminoacid') for character in unknown_characters
]
return zip(letter_codes, unknown_characters)
def nucleotide_degenerate():
return LetterCode('K', 'nucleotide')