--- a/fasta-dinucleotide-shuffle.py	Sat Mar 10 08:17:36 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,223 +0,0 @@
-#!/usr/bin/python
-
-import sys, string, random
-import sequence
-
-# 
-# turn on psyco to speed up by 3X
-#
-if __name__=='__main__': 
-  try:
-    import psyco
-    #psyco.log()
-    psyco.full()
-    psyco_found = True
-  except ImportError:
-#    psyco_found = False
-    pass
-#  print >> sys.stderr, "psyco_found", psyco_found
-
-
-# altschulEriksonDinuclShuffle.py
-# P. Clote, Oct 2003
-
-def computeCountAndLists(s):
-
-  #Initialize lists and mono- and dinucleotide dictionaries
-  List = {} #List is a dictionary of lists
-  List['A'] = []; List['C'] = [];
-  List['G'] = []; List['T'] = [];
-  # FIXME: is this ok?
-  List['N'] = []
-  nuclList   = ["A","C","G","T","N"]
-  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):
-  z = random.random()
-  denom=dinuclCnt[x]['A']+dinuclCnt[x]['C']+dinuclCnt[x]['G']+dinuclCnt[x]['T']+dinuclCnt[x]['N']
-  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'
-  numerator += dinuclCnt[x]['T']
-  if z < float(numerator)/float(denom):
-    dinuclCnt[x]['T'] -= 1
-    return 'T'
-  dinuclCnt[x]['N'] -= 1
-  return 'N'
-
-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(3):
-    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","N"]:
-    if x in s: nuclList.append(x)
-  #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
- 
-def main():
-
-	#
-	# defaults
-	#
-	file_name = None
-	seed = 1
-	copies = 1
-
-	#
-	# get command line arguments
-	#
-	usage = """USAGE: 
-	%s [options]
-
-        -f <filename>   file name (required)
-        -t <tag>        added to shuffled sequence names
-        -s <seed>	random seed; default: %d
-	-c <n>		make <n> shuffled copies of each sequence; default: %d
-        -h              print this usage message
-	""" % (sys.argv[0], seed, copies)
-
-        # no arguments: print usage
-	if len(sys.argv) == 1:
-		print >> sys.stderr, usage; sys.exit(1)
-
-        tag = "";
-
-        # parse command line
-        i = 1
-        while i < len(sys.argv):
-                arg = sys.argv[i]
-                if (arg == "-f"):
-                        i += 1
-                        try: file_name = sys.argv[i]
-                        except: print >> sys.stderr, usage; sys.exit(1)
-                elif (arg == "-t"):
-                        i += 1
-                        try: tag = sys.argv[i]
-                        except: print >> sys.stderr, usage; sys.exit(1)
-                elif (arg == "-s"):
-                        i += 1
-                        try: seed = string.atoi(sys.argv[i])
-                        except: print >> sys.stderr, usage; sys.exit(1)
-                elif (arg == "-c"):
-                        i += 1
-                        try: copies = string.atoi(sys.argv[i])
-                        except: print >> sys.stderr, usage; sys.exit(1)
-                elif (arg == "-h"):
-                        print >> sys.stderr, usage; sys.exit(1)
-                else:
-                        print >> sys.stderr, "Unknown command line argument: " + arg
-                        sys.exit(1)
-                i += 1
-
-        # check that required arguments given
-        if (file_name == None):
-        	print >> sys.stderr, usage; sys.exit(1)
-
-	random.seed(seed)
-
-	# read sequences
-	seqs = sequence.readFASTA(file_name,'Extended DNA')
-
-	for s in seqs:
-		str = s.getString()
-		#FIXME altschul can't handle ambigs
-		name = s.getName()
-
-		#print >> sys.stderr, ">%s" % name
-
-		for i in range(copies):
-
-			shuffledSeq = dinuclShuffle(str)
-
-			if (copies == 1):
-				print >> sys.stdout, ">%s\n%s" % (name+tag, shuffledSeq)
-			else:
-				print >> sys.stdout, ">%s_%d\n%s" % (name+tag, i, shuffledSeq)
-	
-if __name__ == '__main__': main()