### view tools/mytools/altschulEriksonDinuclShuffle.py @ 1:cdcb0ce84a1b

author xuebing Fri, 09 Mar 2012 19:45:15 -0500 9071e359b9a3
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```
#! /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
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)
```