--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/mytools/shuffleSequenceUsingAltschulErikson.txt	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,61 @@
+#! /usr/bin/env python
+
+#shuffleSequenceUsingAltschulErikson.py
+#P. Clote, Oct 2003
+
+#------------------------------------------------------------------
+#Input RNAs in FASTA file, and compute NUM many shufflings of RNA sequence
+#using Altman-Erikson randomly shuffled dinucleotide method.
+#------------------------------------------------------------------
+
+PRINT   = 0
+LINELEN = 70
+
+import sys,os,stats,string
+from altschulEriksonDinuclShuffle import dinuclShuffle
+import computeRNAfoldEnergyForRNAsInFile
+
+
+
+
+def file2string(fileName):
+  file = open(fileName,"r")
+  L = []
+  line = file.readline()
+  while line:
+    while line[0]==">":  # treat lines beginning with '>' as comment and skip 
+      line = file.readline()
+      continue
+    else: 
+      line = line[:-1]
+      L.append(line)
+      line = file.readline()
+  text = string.join(L,"")
+  return text
+
+
+def main(fileName,NUM):
+  seq = file2string(fileName)
+  for i in range(NUM):
+    shuffledSeq = dinuclShuffle(seq) 
+    sys.stdout.write(">%d\n" % (i+1))
+    sys.stdout.write("%s\n" % shuffledSeq)
+
+
+
+  
+if __name__ == '__main__':  
+  if len(sys.argv) < 3 :
+     print "Usage: %s RNAs.faa NUM" %  sys.argv[0]
+     text = """
+            1) RNA.faa is FASTA file of ONE RNA sequence
+            2) NUM is number of random sequences to generate by
+               shuffling the dinucleotides of RNAs input
+     Script to compute Altman-Erikson randomly shuffled dinucleotides.
+            """
+     print text
+     sys.exit(1)
+  fileName = sys.argv[1]
+  NUM      = int(sys.argv[2])
+  main(fileName,NUM)
+