--- /dev/null
+# Copyright 2002 by Yves Bastide and Brad Chapman.
+# 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 binascii import crc32 as _crc32
+
+def crc32(seq) :
+ """Returns the crc32 checksum for a sequence (string or Seq object)"""
+ try :
+ #Assume its a Seq object
+ return _crc32(seq.tostring())
+ except AttributeError :
+ #Assume its a string
+ return _crc32(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 |= (1L << 31)
+ part_h >>= 1L
+ if rflag: part_h ^= 0xd8000000L
+ _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)"""
+ 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 """
+ index = checksum = 0
+ if type(seq)!=type("aa"):
+ seq=seq.tostring()
+ 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.
+ For more information about SEGUID, see:
+ http://bioinformatics.anl.gov/seguid/
+ DOI: 10.1002/pmic.200600032 """
+ try:
+ #Python 2.5 sha1 is in hashlib
+ import hashlib
+ m = hashlib.sha1()
+ except:
+ #For older versions
+ import sha
+ m = sha.new()
+ import base64
+ if type(seq)!=type("aa"):
+ seq=seq.tostring().upper()
+ else:
+ seq=seq.upper()
+ m.update(seq)
+ try:
+ #For Python 2.5
+ return base64.b64encode(m.digest()).rstrip("=")
+ except:
+ #For older versions
+ import os
+ #Note: Using os.linesep doesn't work on Windows,
+ #where os.linesep= "\r\n" but the encoded string
+ #contains "\n" but not "\r\n"
+ return base64.encodestring(m.digest()).replace("\n","").rstrip("=")
+
+if __name__ == "__main__" :
+ print "Quick self test"
+
+ str_light_chain_one = "QSALTQPASVSGSPGQSITISCTGTSSDVGSYNLVSWYQQHPGK" \
+ + "APKLMIYEGSKRPSGVSNRFSGSKSGNTASLTISGLQAEDEADY" \
+ + "YCSSYAGSSTLVFGGGTKLTVL"
+
+ str_light_chain_two = "QSALTQPASVSGSPGQSITISCTGTSSDVGSYNLVSWYQQHPGK" \
+ + "APKLMIYEGSKRPSGVSNRFSGSKSGNTASLTISGLQAEDEADY" \
+ + "YCCSYAGSSTWVFGGGTKLTVL"
+
+ assert crc64(str_light_chain_one) == crc64(str_light_chain_two)
+ assert 'CRC-44CAAD88706CC153' == crc64(str_light_chain_one)
+
+ assert 'BpBeDdcNUYNsdk46JoJdw7Pd3BI' == seguid(str_light_chain_one)
+ assert 'X5XEaayob1nZLOc7eVT9qyczarY' == seguid(str_light_chain_two)
+
+ print "Done"