--- a/altschulEriksonDinuclShuffle.py	Sat Mar 10 08:17:36 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,150 +0,0 @@
-#! /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)