altschulEriksonDinuclShuffle.py

# 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("T","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