Source Code for Module Bio.SeqUtils.CheckSum

  1  # Copyright 2002 by Yves Bastide and Brad Chapman. 
  2  # Copyright 2007 by Sebastian Bassi 
  3  # All rights reserved. 
  4  # This code is part of the Biopython distribution and governed by its 
  5  # license.  Please see the LICENSE file that should have been included 
  6  # as part of this package. 
  7   
  8  """Functions to calculate assorted sequence checksums.""" 
  9   
 10  # crc32, crc64, gcg, and seguid 
 11  # crc64 is adapted from BioPerl 
 12   
 13  from binascii import crc32 as _crc32 
 14  from Bio._py3k import _as_bytes 
 15   
 16   
 17 -def crc32(seq): 
 18      """Returns the crc32 checksum for a sequence (string or Seq object).""" 
 19      #NOTE - On Python 2 returns a signed int, on Python 3 it is unsigned 
 20      #Docs suggest should use crc32(x) & 0xffffffff for consistency. 
 21      #TODO - Should we return crc32(x) & 0xffffffff here? 
 22      try: 
 23          #Assume its a Seq object 
 24          return _crc32(_as_bytes(str(seq))) 
 25      except AttributeError: 
 26          #Assume its a string/unicode 
 27          return _crc32(_as_bytes(seq)) 
 28   
 29   
 30 -def _init_table_h(): 
 31      _table_h = [] 
 32      for i in range(256): 
 33          l = i 
 34          part_h = 0 
 35          for j in range(8): 
 36              rflag = l & 1 
 37              l >>= 1 
 38              if part_h & 1: 
 39                  l |= (1L << 31) 
 40              part_h >>= 1L 
 41              if rflag: 
 42                  part_h ^= 0xd8000000L 
 43          _table_h.append(part_h) 
 44      return _table_h 
 45   
 46  # Initialisation 
 47  _table_h = _init_table_h() 
 48   
 49   
 50 -def crc64(s): 
 51      """Returns the crc64 checksum for a sequence (string or Seq object).""" 
 52      crcl = 0 
 53      crch = 0 
 54      for c in s: 
 55          shr = (crch & 0xFF) << 24 
 56          temp1h = crch >> 8 
 57          temp1l = (crcl >> 8) | shr 
 58          idx = (crcl ^ ord(c)) & 0xFF 
 59          crch = temp1h ^ _table_h[idx] 
 60          crcl = temp1l 
 61   
 62      return "CRC-%08X%08X" % (crch, crcl) 
 63   
 64   
 65 -def gcg(seq): 
 66      """Returns the GCG checksum (int) for a sequence (string or Seq object). 
 67   
 68      Given a nucleotide or amino-acid secuence (or any string), 
 69      returns the GCG checksum (int). Checksum used by GCG program. 
 70      seq type = str. 
 71      Based on BioPerl GCG_checksum. Adapted by Sebastian Bassi 
 72      with the help of John Lenton, Pablo Ziliani, and Gabriel Genellina. 
 73      All sequences are converted to uppercase """ 
 74      try: 
 75          #Assume its a Seq object 
 76          seq = str(seq) 
 77      except AttributeError: 
 78          #Assume its a string 
 79          pass 
 80      index = checksum = 0 
 81      for char in seq: 
 82          index += 1 
 83          checksum += index * ord(char.upper()) 
 84          if index == 57: 
 85              index = 0 
 86      return checksum % 10000 
 87   
 88   
 89 -def seguid(seq): 
 90      """Returns the SEGUID (string) for a sequence (string or Seq object). 
 91   
 92      Given a nucleotide or amino-acid secuence (or any string), 
 93      returns the SEGUID string (A SEquence Globally Unique IDentifier). 
 94      seq type = str. 
 95      For more information about SEGUID, see: 
 96      http://bioinformatics.anl.gov/seguid/ 
 97      DOI: 10.1002/pmic.200600032 """ 
 98      import hashlib 
 99      import base64 
100      m = hashlib.sha1() 
101      try: 
102          #Assume it's a Seq object 
103          seq = str(seq) 
104      except AttributeError: 
105          #Assume it's a string 
106          pass 
107      m.update(_as_bytes(seq.upper())) 
108      try: 
109          #For Python 3+ 
110          return base64.encodebytes(m.digest()).decode().replace("\n", "").rstrip("=") 
111      except AttributeError: 
112          pass 
113      # For all other Pythons 
114      return base64.b64encode(m.digest()).rstrip("=") 
115   
116   
117  if __name__ == "__main__": 
118      print "Quick self test" 
119   
120      str_light_chain_one = "QSALTQPASVSGSPGQSITISCTGTSSDVGSYNLVSWYQQHPGK" \ 
121                      + "APKLMIYEGSKRPSGVSNRFSGSKSGNTASLTISGLQAEDEADY" \ 
122                      + "YCSSYAGSSTLVFGGGTKLTVL" 
123   
124      str_light_chain_two = "QSALTQPASVSGSPGQSITISCTGTSSDVGSYNLVSWYQQHPGK" \ 
125                      + "APKLMIYEGSKRPSGVSNRFSGSKSGNTASLTISGLQAEDEADY" \ 
126                      + "YCCSYAGSSTWVFGGGTKLTVL" 
127   
128      assert crc64(str_light_chain_one) == crc64(str_light_chain_two) 
129      assert 'CRC-44CAAD88706CC153' == crc64(str_light_chain_one) 
130   
131      assert 'BpBeDdcNUYNsdk46JoJdw7Pd3BI' == seguid(str_light_chain_one) 
132      assert 'X5XEaayob1nZLOc7eVT9qyczarY' == seguid(str_light_chain_two) 
133   
134      print "Done" 
135