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11
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1 import sys
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2
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3 from altschulEriksonDinuclShuffle import *
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4
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5 def readFastaFile(infile,outfile):
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6
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7 fin = open(infile)
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8 out = open(outfile,'w')
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9
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10 currSeq=''
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11 currSeqname=None
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12 for line in fin:
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13 if '>' in line:
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14 if currSeqname !=None:
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15 out.write(currSeqname+dinuclShuffle(currSeq)+'\n')
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16 currSeqname=None
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17 currSeq=''
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18 currSeqname=line
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19 else:
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20 currSeq=currSeq+line.strip().upper()
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21
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22 if currSeqname!=None:
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23 out.write(currSeqname+dinuclShuffle(currSeq)+'\n')
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24
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25 fin.close()
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26 out.close()
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27
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28 def readrawseq(infile,outfile):
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29 '''
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30 each line is a sequence
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31 '''
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32 fin = open(infile)
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33 out = open(outfile,'w')
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34 for line in fin:
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35 out.write(dinuclShuffle(line.strip().upper())+'\n')
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36 fin.close()
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37 out.close()
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38
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39 def main():
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40 seqfile = sys.argv[1]
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41 outfile = sys.argv[2]
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42 fasta = sys.argv[3]
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43
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44 if fasta == 'fasta':
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45 readFastaFile(seqfile,outfile)
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46 else:
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47 readrawseq(seqfile,outfile)
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48
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49 main()
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