1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
|
# Copyright 2007 by Peter Cock. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
from Bio.SeqUtils.CheckSum import crc32, crc64, gcg, seguid
from Bio.SeqUtils.lcc import lcc_simp, lcc_mult
from Bio.Seq import Seq, MutableSeq
from Bio.Alphabet import single_letter_alphabet
###################
# crc64 collision #
###################
# Example of crc64 collision from Sebastian Bassi using the
# immunoglobulin lambda light chain variable region from Homo 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) :
return "%0.2f" % lcc_simp(s)
def windowed_LCC(s) :
return ", ".join(["%0.2f" % v for v in lcc_mult(s,20)])
for checksum in [crc32, crc64, gcg, seguid, simple_LCC, windowed_LCC] :
#First using a string:
value = checksum(seq_str)
print " %s = %s" % (checksum.__name__, value)
#Secondly check it works with a Seq object
assert value == checksum(Seq(seq_str, single_letter_alphabet))
#Finally check it works with a MutableSeq object
assert value == checksum(MutableSeq(seq_str, single_letter_alphabet))
|
