--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/altschulEriksonDinuclShuffle.py	Sat Mar 31 21:47:59 2012 -0400
@@ -0,0 +1,150 @@
+#! /usr/bin/env python
+
+# altschulEriksonDinuclShuffle.py
+# P. Clote, Oct 2003
+# NOTE: One cannot use function "count(s,word)" to count the number
+# of occurrences of dinucleotide word in string s, since the built-in
+# function counts only nonoverlapping words, presumably in a left to
+# right fashion.
+
+
+import sys,string,random
+
+
+
+def computeCountAndLists(s):
+  #WARNING: Use of function count(s,'UU') returns 1 on word UUU
+  #since it apparently counts only nonoverlapping words UU
+  #For this reason, we work with the indices.
+
+  #Initialize lists and mono- and dinucleotide dictionaries
+  List = {} #List is a dictionary of lists
+  List['A'] = []; List['C'] = [];
+  List['G'] = []; List['T'] = [];
+  nuclList   = ["A","C","G","T"]
+  s       = s.upper()
+  s       = s.replace("U","T")
+  nuclCnt    = {}  #empty dictionary
+  dinuclCnt  = {}  #empty dictionary
+  for x in nuclList:
+    nuclCnt[x]=0
+    dinuclCnt[x]={}
+    for y in nuclList:
+      dinuclCnt[x][y]=0
+
+  #Compute count and lists
+  nuclCnt[s[0]] = 1
+  nuclTotal     = 1
+  dinuclTotal   = 0
+  for i in range(len(s)-1):
+    x = s[i]; y = s[i+1]
+    List[x].append( y )
+    nuclCnt[y] += 1; nuclTotal  += 1
+    dinuclCnt[x][y] += 1; dinuclTotal += 1
+  assert (nuclTotal==len(s))
+  assert (dinuclTotal==len(s)-1)
+  return nuclCnt,dinuclCnt,List
+ 
+ 
+def chooseEdge(x,dinuclCnt):
+  numInList = 0
+  for y in ['A','C','G','T']:
+    numInList += dinuclCnt[x][y]
+  z = random.random()
+  denom=dinuclCnt[x]['A']+dinuclCnt[x]['C']+dinuclCnt[x]['G']+dinuclCnt[x]['T']
+  numerator = dinuclCnt[x]['A']
+  if z < float(numerator)/float(denom):
+    dinuclCnt[x]['A'] -= 1
+    return 'A'
+  numerator += dinuclCnt[x]['C']
+  if z < float(numerator)/float(denom):
+    dinuclCnt[x]['C'] -= 1
+    return 'C'
+  numerator += dinuclCnt[x]['G']
+  if z < float(numerator)/float(denom):
+    dinuclCnt[x]['G'] -= 1
+    return 'G'
+  dinuclCnt[x]['T'] -= 1
+  return 'T'
+
+def connectedToLast(edgeList,nuclList,lastCh):
+  D = {}
+  for x in nuclList: D[x]=0
+  for edge in edgeList:
+    a = edge[0]; b = edge[1]
+    if b==lastCh: D[a]=1
+  for i in range(2):
+    for edge in edgeList:
+      a = edge[0]; b = edge[1]
+      if D[b]==1: D[a]=1
+  ok = 0
+  for x in nuclList:
+    if x!=lastCh and D[x]==0: return 0
+  return 1
+
+ 
+
+def eulerian(s):
+  nuclCnt,dinuclCnt,List = computeCountAndLists(s)
+  #compute nucleotides appearing in s
+  nuclList = []
+  for x in ["A","C","G","T"]:
+    if x in s: nuclList.append(x)
+  #compute numInList[x] = number of dinucleotides beginning with x
+  numInList = {}
+  for x in nuclList:
+    numInList[x]=0
+    for y in nuclList:
+      numInList[x] += dinuclCnt[x][y]
+  #create dinucleotide shuffle L 
+  firstCh = s[0]  #start with first letter of s
+  lastCh  = s[-1]
+  edgeList = []
+  for x in nuclList:
+    if x!= lastCh: edgeList.append( [x,chooseEdge(x,dinuclCnt)] )
+  ok = connectedToLast(edgeList,nuclList,lastCh)
+  return ok,edgeList,nuclList,lastCh
+
+
+def shuffleEdgeList(L):
+  n = len(L); barrier = n
+  for i in range(n-1):
+    z = int(random.random() * barrier)
+    tmp = L[z]
+    L[z]= L[barrier-1]
+    L[barrier-1] = tmp
+    barrier -= 1
+  return L
+
+def dinuclShuffle(s):
+  ok = 0
+  while not ok:
+    ok,edgeList,nuclList,lastCh = eulerian(s)
+  nuclCnt,dinuclCnt,List = computeCountAndLists(s)
+
+  #remove last edges from each vertex list, shuffle, then add back
+  #the removed edges at end of vertex lists.
+  for [x,y] in edgeList: List[x].remove(y)
+  for x in nuclList: shuffleEdgeList(List[x])
+  for [x,y] in edgeList: List[x].append(y)
+
+  #construct the eulerian path
+  L = [s[0]]; prevCh = s[0]
+  for i in range(len(s)-2):
+    ch = List[prevCh][0] 
+    L.append( ch )
+    del List[prevCh][0]
+    prevCh = ch
+  L.append(s[-1])
+  t = string.join(L,"")
+  return t
+ 
+ 
+
+if __name__ == '__main__':
+  if len(sys.argv)!=3:
+    print "Usage: python altschulEriksonDinuclShuffle.py GCATCGA 5"
+    sys.exit(1)
+  s = sys.argv[1].upper()
+  for i in range(int(sys.argv[2])):
+    print dinuclShuffle(s)