def generateCorrectSequences(groups: int, samples: int, length: int):
# correct sequences
# powtórz względem ilości grup
assert samples >= 2
result = []
for i in range(groups):
# wygeneruj sample -1 losowo
rows = generateSequences(samples - 1, length)
# sprawdz czekerem gdzie jest False
checker = checkAlgorithm(rows, True)
# losuj slowo
last_row = generateSequences(1, length)[0]
# na false zamień na 'A'
for j in range(length):
if not checker[j]:
s = ''.join(r[j] for r in rows)
if s.__contains__('T'):
letter = 'C'
elif s.__contains__('C'):
letter = 'T'
else:
letter = 'A'
last_row = last_row[:j] + letter + last_row[min(j+1,length):]
rows += [last_row]
result += rows
# przelosuj kolejność
random.shuffle(result)
return result
def _checkGroup(self, group):
converted = []
for sample in group:
txt = self.content['i7'][sample[0]]
if self.i5 is not None:
txt += self.content['i5'][sample[1]]
converted.append(txt)
return ac.checkAlgorithm(converted)
def test_CT_valid(self):
self.assertTrue(checkAlgorithm(['C', 'T']))
def test_A_valid(self):
self.assertTrue(checkAlgorithm('A'))
def test_illumina_example_not_extra_data(self):
self.assertEqual(
checkAlgorithm(['GCTACGCT', 'GTAGAGGA', 'GGAGCTAC'], True),
[False, True, True, True, True, False, True, True])
def test_illumina_example_extra_data(self):
self.assertEqual(
checkAlgorithm(['ATTCAGAA', 'GAATTCGT', 'AGCGATAG'], True),
[True, True, True, True, True, True, True, True])
def test_CT_extra_data(self):
self.assertEqual(checkAlgorithm(['C', 'T'], True), [True])
def test_A_extra_data(self):
self.assertEqual(checkAlgorithm('A', True), [True])
def test_illumina_example_not_valid(self):
self.assertFalse(checkAlgorithm(['GCTACGCT', 'GTAGAGGA', 'GGAGCTAC']))
def test_illumina_example_valid(self):
self.assertTrue(checkAlgorithm(['ATTCAGAA', 'GAATTCGT', 'AGCGATAG']))