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1 '''
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2 usage:
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3
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4 python endbias.py utr5-coverage utr3-coverage outputfile
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5 '''
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6 import sys,math
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7
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8 def getCoverage(filename):
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9 f = open(filename)
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10 coverage = {}
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11 for line in f:
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12 flds = line.strip().split('\t')
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13 score = float(flds[4])
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14 name = (flds[0].split('utr'))[0].strip('_')
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15 if coverage.has_key(name):
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16 if score > coverage[name]:
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17 coverage[name] = score
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18 else:
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19 coverage[name] = score
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20 return coverage
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21
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22 def endBias(filename,utr5,utr3):
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23 out = open(filename,'w')
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24 for txpt in utr5.keys():
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25 if utr3.has_key(txpt):
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26 out.write('\t'.join([txpt,str(utr5[txpt]),str(utr3[txpt]),str(math.log((1+utr5[txpt])/(1+utr3[txpt]),2))])+'\n')
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27 out.close()
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28
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29
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30 utr5 = getCoverage(sys.argv[1])
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31 utr3 = getCoverage(sys.argv[2])
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32 endBias(sys.argv[3],utr5,utr3)
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33
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34 '''
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35
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36 utr5 = getCoverage('hmga2-utr5.coverage')
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37 utr3 = getCoverage('hmga2-utr3.coverage')
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38 logratio, cov5,cov3= endBias(utr5,utr3)
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39 2**pylab.median(logratio.values())
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40
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41 log2utr5 = pylab.log2(pylab.array(cov5)+1)
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42 log2utr3 = pylab.log2(pylab.array(cov3)+1)
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43
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44 pylab.plot(log2utr5,log2utr3,'bo')
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45
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46 pylab.show()
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47
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48 utr5 = getCoverage('control-utr5.coverage')
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49 utr3 = getCoverage('control-utr3.coverage')
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50 logratio, cov5,cov3= endBias(utr5,utr3)
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51 2**pylab.median(logratio.values())
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52 '''
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