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[jabaws.git] / website / archive / binaries / mac / src / disembl / biopython-1.50 / Bio / SeqUtils / CheckSum.py

diff --git a/website/archive/binaries/mac/src/disembl/biopython-1.50/Bio/SeqUtils/CheckSum.py b/website/archive/binaries/mac/src/disembl/biopython-1.50/Bio/SeqUtils/CheckSum.py
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+# 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"