def test_crc_checksum_collision(self):
#Explicit testing of crc64 collision:
self.assertNotEqual(self.str_light_chain_one, self.str_light_chain_two)
self.assertNotEqual(crc32(self.str_light_chain_one), crc32(self.str_light_chain_two))
self.assertEqual(crc64(self.str_light_chain_one), crc64(self.str_light_chain_two))
self.assertNotEqual(gcg(self.str_light_chain_one), gcg(self.str_light_chain_two))
self.assertNotEqual(seguid(self.str_light_chain_one), seguid(self.str_light_chain_two))
def test_crc_checksum_collision(self):
# Explicit testing of crc64 collision:
self.assertNotEqual(self.str_light_chain_one, self.str_light_chain_two)
self.assertNotEqual(crc32(self.str_light_chain_one), crc32(self.str_light_chain_two))
self.assertEqual(crc64(self.str_light_chain_one), crc64(self.str_light_chain_two))
self.assertNotEqual(gcg(self.str_light_chain_one), gcg(self.str_light_chain_two))
self.assertNotEqual(seguid(self.str_light_chain_one), seguid(self.str_light_chain_two))
def seq_checksums(
self,
seq_str,
exp_crc32,
exp_crc64,
exp_gcg,
exp_seguid,
exp_simple_LCC,
exp_window_LCC,
):
for s in [seq_str, Seq(seq_str), MutableSeq(seq_str)]:
self.assertEqual(exp_crc32, crc32(s))
self.assertEqual(exp_crc64, crc64(s))
self.assertEqual(exp_gcg, gcg(s))
self.assertEqual(exp_seguid, seguid(s))
self.assertAlmostEqual(exp_simple_LCC, lcc_simp(s), places=2)
values = lcc_mult(s, 20)
self.assertEqual(len(exp_window_LCC), len(values))
for value1, value2 in zip(exp_window_LCC, values):
self.assertAlmostEqual(value1, value2, places=2)
# crc64 collision #
###################
# Example of crc64 collision from Sebastian Bassi using the
# immunoglobulin lambda light chain variable region from H**o sapiens
# Both sequences share the same CRC64 checksum: 44CAAD88706CC153
str_light_chain_one = "QSALTQPASVSGSPGQSITISCTGTSSDVGSYNLVSWYQQHPGK" \
+ "APKLMIYEGSKRPSGVSNRFSGSKSGNTASLTISGLQAEDEADY" \
+ "YCSSYAGSSTLVFGGGTKLTVL"
str_light_chain_two = "QSALTQPASVSGSPGQSITISCTGTSSDVGSYNLVSWYQQHPGK" \
+ "APKLMIYEGSKRPSGVSNRFSGSKSGNTASLTISGLQAEDEADY" \
+ "YCCSYAGSSTWVFGGGTKLTVL"
#Explicit testing of crc64 collision:
assert str_light_chain_one != str_light_chain_two
assert crc32(str_light_chain_one) != crc32(str_light_chain_two)
assert crc64(str_light_chain_one) == crc64(str_light_chain_two)
assert gcg(str_light_chain_one) != gcg(str_light_chain_two)
assert seguid(str_light_chain_one) != seguid(str_light_chain_two)
###########################
# main checksum/LCC tests #
###########################
#Print some output, which the test harness will check
examples = [str_light_chain_one, str_light_chain_two,
"ATGCGTATCGATCGCGATACGATTAGGCGGAT"]
for i, seq_str in enumerate(examples):
print "Example %i, length %i, %s..." % (i+1, len(seq_str), seq_str[:10])
def u_crc32(seq):
#NOTE - On Python 2 crc32 could return a signed int, but on Python 3 it is
#always unsigned
#Docs suggest should use crc32(x) & 0xffffffff for consistency.
return crc32(seq) & 0xffffffff
# crc64 collision #
###################
# Example of crc64 collision from Sebastian Bassi using the
# immunoglobulin lambda light chain variable region from H**o sapiens
# Both sequences share the same CRC64 checksum: 44CAAD88706CC153
str_light_chain_one = "QSALTQPASVSGSPGQSITISCTGTSSDVGSYNLVSWYQQHPGK" \
+ "APKLMIYEGSKRPSGVSNRFSGSKSGNTASLTISGLQAEDEADY" \
+ "YCSSYAGSSTLVFGGGTKLTVL"
str_light_chain_two = "QSALTQPASVSGSPGQSITISCTGTSSDVGSYNLVSWYQQHPGK" \
+ "APKLMIYEGSKRPSGVSNRFSGSKSGNTASLTISGLQAEDEADY" \
+ "YCCSYAGSSTWVFGGGTKLTVL"
#Explicit testing of crc64 collision:
assert str_light_chain_one != str_light_chain_two
assert crc32(str_light_chain_one) != crc32(str_light_chain_two)
assert crc64(str_light_chain_one) == crc64(str_light_chain_two)
assert gcg(str_light_chain_one) != gcg(str_light_chain_two)
assert seguid(str_light_chain_one) != seguid(str_light_chain_two)
###########################
# main checksum/LCC tests #
###########################
#Print some output, which the test harness will check
examples = [str_light_chain_one, str_light_chain_two,
"ATGCGTATCGATCGCGATACGATTAGGCGGAT"]
for i, seq_str in enumerate(examples) :
print "Example %i, length %i, %s..." % (i+1, len(seq_str), seq_str[:10])
def u_crc32(seq):
#NOTE - On Python 2 crc32 could return a signed int, but on Python 3 it is
#always unsigned
#Docs suggest should use crc32(x) & 0xffffffff for consistency.
return crc32(seq) & 0xffffffff