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# Copyright 2002 by Yves Bastide and Brad Chapman.
# Copyright 2007 by Sebastian Bassi
# 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.
"""Functions to calculate assorted sequence checksums."""
# crc32, crc64, gcg, and seguid
# crc64 is adapted from BioPerl
from __future__ import print_function
from binascii import crc32 as _crc32
from Bio._py3k import _as_bytes
def crc32(seq):
"""Returns the crc32 checksum for a sequence (string or Seq object).
Note that the case is important:
>>> crc32("ACGTACGTACGT")
20049947
>>> crc32("acgtACGTacgt")
1688586483
"""
# NOTE - On Python 2 returns a signed int, on Python 3 it is unsigned
# Docs suggest should use crc32(x) & 0xffffffff for consistency.
# TODO - Should we return crc32(x) & 0xffffffff here?
try:
# Assume its a Seq object
return _crc32(_as_bytes(str(seq)))
except AttributeError:
# Assume its a string/unicode
return _crc32(_as_bytes(seq))
def _init_table_h():
_table_h = []
for i in range(256):
l = i
part_h = 0
for j in range(8):
rflag = l & 1
l >>= 1
if part_h & 1:
l |= (1 << 31)
part_h >>= 1
if rflag:
part_h ^= 0xd8000000
_table_h.append(part_h)
return _table_h
# Initialisation
_table_h = _init_table_h()
def crc64(s):
"""Returns the crc64 checksum for a sequence (string or Seq object).
Note that the case is important:
>>> crc64("ACGTACGTACGT")
'CRC-C4FBB762C4A87EBD'
>>> crc64("acgtACGTacgt")
'CRC-DA4509DC64A87EBD'
"""
crcl = 0
crch = 0
for c in s:
shr = (crch & 0xFF) << 24
temp1h = crch >> 8
temp1l = (crcl >> 8) | shr
idx = (crcl ^ ord(c)) & 0xFF
crch = temp1h ^ _table_h[idx]
crcl = temp1l
return "CRC-%08X%08X" % (crch, crcl)
def gcg(seq):
"""Returns the GCG checksum (int) for a sequence (string or Seq object).
Given a nucleotide or amino-acid secuence (or any string),
returns the GCG checksum (int). Checksum used by GCG program.
seq type = str.
Based on BioPerl GCG_checksum. Adapted by Sebastian Bassi
with the help of John Lenton, Pablo Ziliani, and Gabriel Genellina.
All sequences are converted to uppercase.
>>> gcg("ACGTACGTACGT")
5688
>>> gcg("acgtACGTacgt")
5688
"""
try:
# Assume its a Seq object
seq = str(seq)
except AttributeError:
# Assume its a string
pass
index = checksum = 0
for char in seq:
index += 1
checksum += index * ord(char.upper())
if index == 57:
index = 0
return checksum % 10000
def seguid(seq):
"""Returns the SEGUID (string) for a sequence (string or Seq object).
Given a nucleotide or amino-acid secuence (or any string),
returns the SEGUID string (A SEquence Globally Unique IDentifier).
seq type = str.
Note that the case is not important:
>>> seguid("ACGTACGTACGT")
'If6HIvcnRSQDVNiAoefAzySc6i4'
>>> seguid("acgtACGTacgt")
'If6HIvcnRSQDVNiAoefAzySc6i4'
For more information about SEGUID, see:
http://bioinformatics.anl.gov/seguid/
DOI: 10.1002/pmic.200600032
"""
import hashlib
import base64
m = hashlib.sha1()
try:
# Assume it's a Seq object
seq = str(seq)
except AttributeError:
# Assume it's a string
pass
m.update(_as_bytes(seq.upper()))
try:
# For Python 3+
return base64.encodebytes(m.digest()).decode().replace("\n", "").rstrip("=")
except AttributeError:
pass
# For all other Pythons
return base64.b64encode(m.digest()).rstrip("=")
if __name__ == "__main__":
from Bio._utils import run_doctest
run_doctest()
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