def test_hamming_dist_timing(self):
list_of_strings = [string_generator() for i in range(10)]
print(list_of_strings)
string_result = []
string_start = time.process_time_ns()
for s1 in list_of_strings:
for s2 in list_of_strings:
string_result.append(naive_hamming_distance(s1, s2))
string_end = time.process_time_ns()
print(f'no of mismatches = {string_result}')
print("string hamming: {:,}".format(string_end - string_start))
binary_result = []
binary_start = time.process_time_ns()
for s1 in list_of_strings:
for s2 in list_of_strings:
binary_result.append(hamming_distance(s1, s2))
binary_end = time.process_time_ns()
print("binary hamming: {:,}".format(binary_end - binary_start))
list_of_preprocessed_binaries = []
for s in list_of_strings:
list_of_preprocessed_binaries.append(string_to_hamming_binary(s))
binary_result_pre = []
binary_start_pre = time.process_time_ns()
for s1 in list_of_preprocessed_binaries:
for s2 in list_of_preprocessed_binaries:
binary_result_pre.append(binary_hamming_dist_calc(s1, s2))
binary_end_pre = time.process_time_ns()
print("prepro hamming: {:,}".format(binary_end_pre - binary_start_pre))
self.assertEqual(string_result, binary_result)
self.assertEqual(binary_result_pre, binary_result)
def hamming_distance_max_stop(string1, string2, max_dist):
b1 = string_to_hamming_binary(string1)
b2 = string_to_hamming_binary(string2)
return binary_hamming_dist_calc_max_stop(b1, b2, max_dist)
def test_longerererer_string_to_binary(self):
self.assertEqual(
0b0100000100101000100000010001001010001000000100010010100010000001010000010010100010000001000100101000100000010001001010001000000101000001001010001000000100010010100010000001000100101000100000010100000100101000100000010001001010001000000100010010100010000001010000010010100010000001000100101000100000010001001010001000000101000001001010001000000100010010100010000001000100101000100000010100000100101000100000010001001010001000000100010010100010000001010000010010100010000001000100101000100000010001001010001000000101000001001010001000000100010010100010000001000100101000100000010100000100101000100000010001001010001000000100010010100010000001010000010010100010000001000100101000100000010001001010001000000101000001001010001000000100010010100010000001000100101000100000010100000100101000100000010001001010001000000100010010100010000001010000010010100010000001000100101000100000010001001010001000000101000001001010001000000100010010100010000001000100101000100000010100000100101000100000010001001010001000000100010010100010000001,
string_to_hamming_binary(
'GACTTAACTTAACTTAGACTTAACTTAACTTAGACTTAACTTAACTTAGACTTAACTTAACTTAGACTTAACTTAACTTAGACTTAACTTAACTTAGACTTAACTTAACTTAGACTTAACTTAACTTAGACTTAACTTAACTTAGACTTAACTTAACTTAGACTTAACTTAACTTAGACTTAACTTAACTTAGACTTAACTTAACTTAGACTTAACTTAACTTAGACTTAACTTAACTTAGACTTAACTTAACTTA'
)) # 256 chars
def test_two_letters_to_binary(self):
self.assertEqual(0b00010001, string_to_hamming_binary('AA'))
self.assertEqual(0b00101000, string_to_hamming_binary('CT'))
self.assertEqual(0b01000001, string_to_hamming_binary('GA'))
self.assertEqual(0b10000100, string_to_hamming_binary('TG'))
def test_one_letter_to_binary(self):
self.assertEqual(0b0000, string_to_hamming_binary('*'))
self.assertEqual(0b0001, string_to_hamming_binary('A'))
self.assertEqual(0b0010, string_to_hamming_binary('C'))
self.assertEqual(0b0100, string_to_hamming_binary('G'))
self.assertEqual(0b1000, string_to_hamming_binary('T'))