Delete unneeded directory

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

diff --git a/website/archive/binaries/mac/src/globplot/biopython-1.50/Bio/SeqUtils/CheckSum.py b/website/archive/binaries/mac/src/globplot/biopython-1.50/Bio/SeqUtils/CheckSum.py
deleted file mode 100644 (file)
index ae1a9d6..0000000
--- a/website/archive/binaries/mac/src/globplot/biopython-1.50/Bio/SeqUtils/CheckSum.py
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@@ -1,124 +0,0 @@
-# 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"