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1 '''
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2 find overlap and test signifiance
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3 '''
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4
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5 import os,sys
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6
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7 def lineCount(filename):
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8 if os.stat(filename).st_size == 0:
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9 return 0
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10 with open(filename) as f:
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11 for i, l in enumerate(f):
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12 pass
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13 print i
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14 return i+1
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15
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16 def intersect(fileA,fileB,outfile,fraction,reciprocal):
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17 # return fileA intervals that overlap with interval in fileB
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18 cmd = 'intersectBed -a '+fileA+' -b '+fileB + ' -u -wa -f '+fraction +' '+ reciprocal + '>'+outfile
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19 #print cmd
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20 os.system(cmd)
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21
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22 def shuffle(fileA,fileB,genomefile,fraction,reciprocal,N):
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23 # shuffle fileA N times, return the distribution of overlaps
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24 nOverlap = []
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25 for i in range(N):
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26 # shuffle fileA using shuffleBed
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27 #cmd = 'shuffleBed -i '+fileA+' -g '+genomefile +'>fileA.shuffled'
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28 # using random_interval.py
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29 cmd = 'python /Users/xuebing/galaxy-dist/tools/mytools/random_interval.py '+fileA+' fileA.shuffled across '+genomefile
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30 os.system(cmd)
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31 intersect('fileA.shuffled',fileB,'tmp',fraction,reciprocal)
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32 nOverlap.append(lineCount('tmp'))
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33 os.system('rm tmp')
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34 os.system('rm fileA.shuffled')
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35 return nOverlap
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36
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37 def main():
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38 fileA = sys.argv[1]
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39 fileB = sys.argv[2]
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40 outfile = sys.argv[3]
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41 outplot = sys.argv[4]
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42 outshuffle = sys.argv[5]
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43 N = int(sys.argv[6]) # times to shuffle
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44 genomefile = sys.argv[7]
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45 fraction = sys.argv[8]
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46 if len(sys.argv) == 10:
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47 reciprocal = sys.argv[9] # can only be '-r'
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48 else:
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49 reciprocal = ''
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50
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51 #print sys.argv
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52
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53 # number of lines in input
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54 nA = lineCount(fileA)
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55 nB = lineCount(fileB)
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56
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57 # intersect on real data
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58 intersect(fileA,fileB,outfile,fraction,reciprocal)
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59 # number of overlaps
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60 nOverlapReal = lineCount(outfile)
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61
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62 #print 'number of intervals in inputA that overlap with intervals in inputB:',nOverlapReal
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63
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64 # shuffle fileA to estimate background
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65 nOverlapNull = shuffle(fileA,fileB,genomefile,fraction,reciprocal,N)
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66 out = open(outshuffle,'w')
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67 out.write("\t".join(map(str,nOverlapNull)))
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68 out.close()
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69
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70 # plot histogram
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71 rscript = open('tmp.r','w')
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72 rscript.write("options(warn=-1)\n")
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73 rscript.write("x0 <- "+str(nOverlapReal)+"\n")
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74 rscript.write("x <- c("+','.join(map(str,nOverlapNull))+")\n")
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75 rscript.write("library(MASS)\n")
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76 rscript.write("pv <- min((1+sum(x>=x0))/length(x),(1+sum(x<=x0))/length(x))\n")
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77 rscript.write("title <- paste('actual:chance = ',x0,':',format(mean(x),digits=1,nsmall=1),' = ',format(x0/mean(x),digits=1,nsmall=2),', p-value < ',pv,sep='')\n")
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78 rscript.write("pdf('"+outplot+"')\n")
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79 rscript.write("library(grid)\n")
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80 rscript.write("library(VennDiagram)\n")
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81 rscript.write("venn <- venn.diagram(x=list(A=1:"+str(nA)+",B="+str(nA-nOverlapReal+1)+":"+str(nA+nB-nOverlapReal)+"),filename=NULL,fill=c('red','blue'),col='transparent',alpha=0.5,label.col='black',cex=3,lwd=0,fontfamily='serif',fontface='bold',cat.col = c('red', 'blue'),cat.cex=3,cat.fontfamily='serif',cat.fontface='bold')\n")
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82 rscript.write("grid.draw(venn)\n")
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83 rscript.write("h <- hist(x,breaks=50,xlab='number of overlaps',ylab='frequency',main=title)\n")
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84 rscript.write("plot(h$mids,h$counts,type='h',xlim=c(min(h$mids,x0),max(x0,h$mids)),ylim=c(0,max(h$counts)),xlab='number of overlaps',ylab='frequency',main=title)\n")
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85 rscript.write("points(x0,0,col='red')\n")
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86 rscript.write("dev.off()\n")
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87 rscript.close()
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88 os.system("R --vanilla < tmp.r")
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89 os.system('rm tmp.r')
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90 main()
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