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1 # -*- coding: iso-8859-1 -*-
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2 import random,sys,math
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3
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4 #import pylab
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5
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6 def readMotifFile(filename):
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7
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8 try:
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9 f=open(filename)
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10 except IOError:
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11 print "could not open",filename,"Are you sure this file exists?"
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12 sys.exit(1)
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13
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14 seqs=[]
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15 maxL = 0
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16 for line in f:
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17 if '>' in line or 'N' in line:
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18 next
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19 else:
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20 seq = line.strip().upper()
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21 if maxL < len(seq):
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22 maxL = len(seq)
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23 seqs.append(seq)
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24 f.close()
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25
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26 print len(seqs),'sequences loaded'
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27 print 'max seq length:',maxL
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28 for i in range(len(seqs)):
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29 if len(seqs[i]) < maxL:
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30 del seqs[i]
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31 print len(seqs),'sequences with length = ',maxL
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32 return seqs
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33
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34
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35 def createWeightMatrix(seqs,psuedocont):
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36
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37 motifWidth = len(seqs[0])
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38 weightMatrix = []
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39 for i in range(motifWidth):
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40 weightMatrix.append({'A':psuedocont,'C':psuedocont,'G':psuedocont,'T':psuedocont})
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41
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42 #Use a for loop to iterate through all the sequences. For each sequence, begin at the start site in starts, and look at motifWidth bases. Count how many times each base appears in each position of the motif
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43 #YOUR CODE HERE
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44 for seq in seqs:
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45 for pos in range(motifWidth):
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46 weightMatrix[pos][seq[pos]] = weightMatrix[pos][seq[pos]] + 1.0
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47
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48 #Normalize your weight matrix (so that it contains probabilities rather than counts)
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49 #Remember the added psuedocounts when you normalize!
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50 for pos in range(motifWidth):
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51 totalCount = sum(weightMatrix[pos].values())
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52 for letter in weightMatrix[pos].keys():
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53 weightMatrix[pos][letter] = weightMatrix[pos][letter]/totalCount
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54
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55 #Return your weight matrix
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56 return weightMatrix
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57
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58 def printMemeFormat(weightMatrix,motifName,filename,nSite,background):
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59 f = open(filename,'w')
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60 f.write('MEME version 4.4\n\n')
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61
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62 f.write('ALPHABET= ACGT\n\n')
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63
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64 f.write('strands: + -\n\n')
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65
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66 f.write('Background letter frequencies (from:\n')
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67 f.write(background+'\n\n')
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68
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69 f.write('MOTIF '+motifName+'\n\n')
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70
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71 f.write('letter-probability matrix: alength= 4 '+'w= '+str(len(weightMatrix))+' nsites= '+str(nSite)+' E= 0\n')
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72 for position in range(len(weightMatrix)):
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73 probsThisPosition=weightMatrix[position]
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74 f.write(' '+"%.6f" %(probsThisPosition['A'])+'\t '+"%.6f" %(probsThisPosition['C'])+'\t '+"%.6f" %(probsThisPosition['G'])+'\t '+"%.6f" %(probsThisPosition['T'])+'\t\n')
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75 f.write('\n\n')
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76 f.close()
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77
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78 #get a two decimal-place string representation of a float f
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79 def twoDecimal(f):
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80 return "%.6f" %(f)
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81
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82 def run():
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83
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84 #Get file name from command line
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85 if len(sys.argv) < 3:
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86 print "python seq2meme.py motif_fasta outputfile motifName psuedocont background"
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87 sys.exit(1)
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88 else:
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89 motifFile=sys.argv[1] #
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90 outFile=sys.argv[2]
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91 motifName=sys.argv[3]
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92 psuedocont = float(sys.argv[4])
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93 background=' '.join(sys.argv[5].strip().split(','))
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94
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95 motifs=readMotifFile(motifFile)
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96
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97 #Create weight matrix
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98 motifWeightMatrix=createWeightMatrix(motifs,psuedocont)
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99 printMemeFormat(motifWeightMatrix,motifName,outFile,len(motifs),background)
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100 run()
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101
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