Python gcg Examples

Example #1

File: test_SeqUtils.py Project: Dologan/biopython

 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))

Example #2

 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))

Example #3

File: test_SeqUtils.py Project: Dologan/biopython

 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, single_letter_alphabet),
               MutableSeq(seq_str, single_letter_alphabet)]:
         self.assertEqual(exp_crc32, u_crc32(s))
         self.assertEqual(exp_crc64, crc64(s))
         self.assertEqual(exp_gcg, gcg(s))
         self.assertEqual(exp_seguid, seguid(s))
         self.assertEqual(exp_simple_LCC, simple_LCC(s))
         self.assertEqual(exp_window_LCC, windowed_LCC(s))

Example #4

 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, single_letter_alphabet),
               MutableSeq(seq_str, single_letter_alphabet)]:
         self.assertEqual(exp_crc32, u_crc32(s))
         self.assertEqual(exp_crc64, crc64(s))
         self.assertEqual(exp_gcg, gcg(s))
         self.assertEqual(exp_seguid, seguid(s))
         self.assertEqual(exp_simple_LCC, simple_LCC(s))
         self.assertEqual(exp_window_LCC, windowed_LCC(s))

Example #5

 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, single_letter_alphabet),
               MutableSeq(seq_str, single_letter_alphabet)]:
         self.assertEqual(exp_crc32, u_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)

Example #6

File: test_SeqUtils.py Project: Mat-D/biopython

# 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])

    #Avoid cross platforms with printing floats by doing conversion explicitly
    def simple_LCC(s):

Example #7

File: test_SeqUtils.py Project: manucorreia/biopython

# 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])

    #Avoid cross platforms with printing floats by doing conversion explicitly
    def simple_LCC(s) :