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