--- a/seqshuffle.py	Sat Mar 10 08:17:36 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,49 +0,0 @@
-import sys
-
-from altschulEriksonDinuclShuffle import *
-            
-def readFastaFile(infile,outfile):
-
-    fin = open(infile)
-    out = open(outfile,'w')
-    
-    currSeq=''
-    currSeqname=None
-    for line in fin:
-        if '>' in line:
-            if  currSeqname !=None:
-                out.write(currSeqname+dinuclShuffle(currSeq)+'\n')
-                currSeqname=None
-                currSeq=''
-            currSeqname=line
-        else:
-            currSeq=currSeq+line.strip().upper()
-
-    if currSeqname!=None:
-        out.write(currSeqname+dinuclShuffle(currSeq)+'\n')
-    
-    fin.close()
-    out.close()
-
-def readrawseq(infile,outfile):
-    '''
-    each line is a sequence
-    '''
-    fin = open(infile)
-    out = open(outfile,'w')
-    for line in fin:
-        out.write(dinuclShuffle(line.strip().upper())+'\n')
-    fin.close()
-    out.close()
-    
-def main():
-    seqfile = sys.argv[1]
-    outfile = sys.argv[2]
-    fasta = sys.argv[3]
-
-    if fasta == 'fasta':
-        readFastaFile(seqfile,outfile)
-    else:
-        readrawseq(seqfile,outfile)
-
-main()