# Copyright 2002 by Yves Bastide and Brad Chapman. # Copyright 2007 by Sebastian Bassi # All rights reserved. # This file is part of the Biopython distribution and governed by your # choice of the "Biopython License Agreement" or the "BSD 3-Clause 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): """Return 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): part_l = i part_h = 0 for j in range(8): rflag = part_l & 1 part_l >>= 1 if part_h & 1: part_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): """Return 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): """Return 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): """Return 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/ https://doi.org/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+ tmp = base64.encodebytes(m.digest()) return tmp.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()