--- a/revcompl.py	Sat Mar 10 08:17:36 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,84 +0,0 @@
-import sys
-
-compldna = {'A':'T',
-        'C':'G',
-        'G':'C',
-        'T':'A',
-        'U':'A',
-        'M':'K',
-        'K':'M',
-        'W':'W',
-        'S':'S',
-        'R':'Y',
-        'Y':'R',
-        'N':'N'}
-complrna = {'A':'U',
-        'C':'G',
-        'G':'C',
-        'T':'A',
-        'U':'A',
-        'M':'K',
-        'K':'M',
-        'W':'W',
-        'S':'S',
-        'R':'Y',
-        'Y':'R',
-        'N':'N'}
-def complement(seq,compl):  
-    complseq = [compl[base] for base in seq]  
-    return complseq
-    
-def reverse_complement(seq,compl):  
-    seq = list(seq)  
-    seq.reverse()  
-    return ''.join(complement(seq,compl)) 
-            
-def readFastaFile(infile,outfile,compl):
-
-    fin = open(infile)
-    out = open(outfile,'w')
-    
-    currSeq=''
-    currSeqname=None
-    for line in fin:
-        if '>' in line:
-            if  currSeqname !=None:
-                out.write(currSeqname+reverse_complement(currSeq,compl)+'\n')
-                currSeqname=None
-                currSeq=''
-            currSeqname=line
-        else:
-            currSeq=currSeq+line.strip().upper()
-
-    if currSeqname!=None:
-        out.write(currSeqname+reverse_complement(currSeq,compl)+'\n')
-    
-    fin.close()
-    out.close()
-
-def readrawseq(infile,outfile,compl):
-    '''
-    each line is a sequence
-    '''
-    fin = open(infile)
-    out = open(outfile,'w')
-    for line in fin:
-        out.write(reverse_complement(line.strip().upper(),compl)+'\n')
-    fin.close()
-    out.close()
-    
-def main():
-    seqfile = sys.argv[1]
-    outfile = sys.argv[2]
-    fasta = sys.argv[3]
-    rna = sys.argv[4]
-    if rna == 'rna':
-        compl = complrna
-    else:
-        compl = compldna
-    if fasta == 'fasta':
-        readFastaFile(seqfile,outfile,compl)
-    else:
-        readrawseq(seqfile,outfile,compl)
-
-main()