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11
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1 '''
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2 get binned score of intervals,allow extension
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3 '''
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4
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5 import os,sys,numpy
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6
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7 from resize import *
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8
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9 from bx.bbi.bigwig_file import BigWigFile
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10
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11 def binning(x,n):
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12 # make n bin of x
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13 y = numpy.zeros(n,dtype=float)
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14 if len(x) == 0:
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15 return y
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16 step = float(len(x))/n
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17 for k in range(n):
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18 i = int(step*k)
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19 j = int(step*(k+1)) + 1
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20 y[k] = x[i:j].mean()
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21 #print i,j,k,y[k]
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22 return y
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23
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24 def getBinnedScore(bwfile,intvfile,nbin):
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25 '''
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26 get binned average and std
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27 '''
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28 fbw = open(bwfile)
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29 bw = BigWigFile(file=fbw)
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30 fin = open(intvfile)
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31 avg = numpy.zeros(nbin)
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32 sqr = numpy.zeros(nbin)
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33 N = 0
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34 for line in fin:
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35 #chrom,start,end,name,score,strand
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36 flds = line.strip().split('\t')
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37 #get the score at base resolution as an array
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38 scores = bw.get_as_array(flds[0],int(flds[1]),int(flds[2]))
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39 if scores == None:
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40 print 'not found:\t',line
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41 continue
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42 N = N + 1
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43 #print line,scores
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44 # reverse if on minus strand
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45 if flds[5] == '-':
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46 scores = scores[::-1]
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47 # no score = 0
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48 scores = numpy.nan_to_num(scores)
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49 # bin the data
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50 binned = binning(scores,nbin)
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51 avg = avg + binned
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52 sqr = sqr + binned**2
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53 # compute avg and std
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54 avg = avg / N
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55 err = ((sqr/N-avg**2)**0.5)/(N**0.5)
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56 return avg,err
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57
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58 def getExtendedBinScore(bwfile,intvfile,nbins,exts):
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59 '''
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60 nbins: n1,n2,n3
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61 exts: l1,l2,l3,l4
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62 '''
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63 # make left extension
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64 resize(intvfile,intvfile+'.tmp','start-'+str(exts[0]),'start+'+str(exts[1]),'stranded')
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65 # compute binned average
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66 avg,err = getBinnedScore(bwfile,intvfile+'.tmp',nbins[0])
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67 # make center region
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68 resize(intvfile,intvfile+'.tmp','start+'+str(exts[1]),'end-'+str(exts[2]),'stranded')
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69 # compute binned average
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70 avg1,err1 = getBinnedScore(bwfile,intvfile+'.tmp',nbins[1])
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71 avg = numpy.concatenate((avg,avg1))
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72 err = numpy.concatenate((err,err1))
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73 # make right region
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74 resize(intvfile,intvfile+'.tmp','end-'+str(exts[2]),'end+'+str(exts[3]),'stranded')
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75 # compute binned average
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76 avg2,err2 = getBinnedScore(bwfile,intvfile+'.tmp',nbins[2])
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77 avg = numpy.concatenate((avg,avg2))
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78 err = numpy.concatenate((err,err2))
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79
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80 return avg,err
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81
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82 print sys.argv
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83 bwfile,intvfile,exts,nbins,outfile,outplot = sys.argv
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84 avg, err = getExtendedBinScore(bwfile,intvfile,numpy.fromstring(nbins,sep=','),numpy.fromstring(exts,sep=','))
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85 out = open(outfile,'w')
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86 numpy.savetxt(out, avg, fmt='%.6f', delimiter=' ', newline=' ')
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87 out.write('\n')
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88 numpy.savetxt(out, err, fmt='%.6f', delimiter=' ', newline=' ')
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89 out.write('\n')
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90 out.close()
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91
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92 # plot
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93 rscript = open("tmp.r","w")
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94 rscript.write("options(warn=-1)\n")
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95 rscript.write("x <- read.table('"+outfile+"')\n")
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96 rscript.write("pdf('"+outplot+"')\n")
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97 rscript.write("avg <- x[1,]\n")
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98 rscript.write("err <- x[2,]\n")
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99 rscript.write("print(x)\n")
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100 rscript.write("ylim=c(min(avg-err),max(avg+err))\n")
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101 rscript.write("xticks <- seq(ncol(x))\n")
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102 rscript.write("plot(xticks,avg,ylab='average coverage',type='l',lwd=0,ylim=ylim)\n")
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103 rscript.write("polygon(c(xticks,rev(xticks)),c(avg+err,rev(avg-err)),col='lightgreen',border=NA)\n")
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104 rscript.write("lines(xticks,avg,type='l',lwd=1)\n")
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105 rscript.write("dev.off()\n")
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106 rscript.close()
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107 os.system("R --vanilla < tmp.r")
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108 os.system("rm tmp.r")
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109
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