def test_longest_palindrome_beginning(self):
sequence = GeneticSequence('TGGATCCATTAA')
self.assertEqual(sequence.longest_palindrome.index, 0)
self.assertEqual(sequence.longest_palindrome.sequence.length, 8)
self.assertEqual(sequence.longest_palindrome.sequence, 'TGGATCCA')
sequence = GeneticSequence('AATTC')
self.assertEqual(sequence.longest_palindrome.index, 0)
self.assertEqual(sequence.longest_palindrome.sequence.length, 4)
self.assertEqual(sequence.longest_palindrome.sequence, 'AATT')
def test_longest_palindrome_end(self):
sequence = GeneticSequence('ATTACCTAGGT')
self.assertEqual(sequence.longest_palindrome.index, 3)
self.assertEqual(sequence.longest_palindrome.sequence.length, 8)
self.assertEqual(sequence.longest_palindrome.sequence, 'ACCTAGGT')
sequence = GeneticSequence('CTTAA')
self.assertEqual(sequence.longest_palindrome.index, 1)
self.assertEqual(sequence.longest_palindrome.sequence.length, 4)
self.assertEqual(sequence.longest_palindrome.sequence, 'TTAA')
def test_longest_palindrome_middle(self):
# Between shorter palindromes.
sequence = GeneticSequence('TTAATGGATCCACCGG')
self.assertEqual(sequence.longest_palindrome.index, 4)
self.assertEqual(sequence.longest_palindrome.sequence.length, 8)
self.assertEqual(sequence.longest_palindrome.sequence, 'TGGATCCA')
sequence = GeneticSequence('GCAATTCG')
self.assertEqual(sequence.longest_palindrome.index, 2)
self.assertEqual(sequence.longest_palindrome.sequence.length, 4)
self.assertEqual(sequence.longest_palindrome.sequence, 'AATT')
def test_is_palindrome(self):
self.assertTrue(GeneticSequence('ACCTAGGT').is_palindrome)
self.assertTrue(GeneticSequence('TGGATCCA').is_palindrome)
self.assertTrue(GeneticSequence('TTAA').is_palindrome)
self.assertTrue(GeneticSequence('CCGG').is_palindrome)
self.assertTrue(GeneticSequence('AT').is_palindrome)
self.assertTrue(GeneticSequence('CG').is_palindrome)
self.assertFalse(GeneticSequence('TTACCTAGGT').is_palindrome)
self.assertFalse(GeneticSequence('CTTAA').is_palindrome)
self.assertFalse(GeneticSequence('ATTA').is_palindrome)
def print_longest_palindrome(sequence_string):
try:
sequence = GeneticSequence(sequence_string)
except GeneticSequence.InvalidSequenceError as e:
print(f'\n{e}\n')
else:
pal = sequence.longest_palindrome
if pal.sequence:
print(f'\nStarting Index: {pal.index}')
print(f'Length: {pal.sequence.length}')
print(f'Palindrome: "{pal.sequence}"\n')
else:
print('\nNo palindrome found\n')
def test_longest_palindrome_self(self):
sequence = GeneticSequence('TTAA')
self.assertEqual(sequence.longest_palindrome.index, 0)
self.assertIs(sequence.longest_palindrome.sequence, sequence)
def test_longest_palindrome_none(self):
sequence = GeneticSequence('ACTG')
self.assertIsNone(sequence.longest_palindrome.sequence)
self.assertIsNone(sequence.longest_palindrome.index)
def test_complement(self):
self.assertEqual(GeneticSequence('ATCG').complement, 'TAGC')
def test_case_insensitive(self):
self.assertEqual(GeneticSequence('atcg'), 'ATCG')
self.assertEqual(GeneticSequence('gCtA'), 'GCTA')