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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 i = 0
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9 with open(filename) as f:
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10 for i, l in enumerate(f):
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11 pass
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12 return i + 1
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13
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14 def intersect(fileA,fileB,outfile,fraction,reciprocal):
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15 # return fileA intervals that overlap with interval in fileB
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16 cmd = 'intersectBed -a '+fileA+' -b '+fileB + ' --wo -f '+fraction +' '+ reciprocal + '>'+outfile
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17 #print cmd
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18 os.system(cmd)
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19
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20 def parseIntersect(filename):
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21 # get number of overlapped A and B
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22 nA = 0
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23 nB = 0
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24 return nA,nb
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25
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26 def shuffle(fileA,fileB,genomefile,fraction,reciprocal,N):
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27 # shuffle fileA N times, return the distribution of overlaps
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28 nOverlap = []
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29 for i in range(N):
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30 # shuffle fileA using shuffleBed
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31 #cmd = 'shuffleBed -i '+fileA+' -g '+genomefile +'>fileA.shuffled'
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32 # using random_interval.py
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33 cmd = 'python /Users/xuebing/galaxy-dist/tools/mytools/random_interval.py '+fileA+' fileA.shuffled across '+genomefile
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34 os.system(cmd)
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35 intersect('fileA.shuffled',fileB,'tmp',fraction,reciprocal)
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36 nOverlap.append(lineCount('tmp'))
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37 os.system('rm tmp')
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38 os.system('rm fileA.shuffled')
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39 return nOverlap
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40
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41 def main():
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42 fileA = sys.argv[1]
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43 fileB = sys.argv[2]
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44 outfile = sys.argv[3]
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45 outplot = sys.argv[4]
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46 N = int(sys.argv[5]) # times to shuffle
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47 genomefile = sys.argv[6]
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48 fraction = sys.argv[7]
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49 if len(sys.argv) == 9:
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50 reciprocal = sys.argv[8] # can only be '-r'
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51 else:
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52 reciprocal = ''
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53
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54 print sys.argv
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55
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56 # intersect on real data
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57 intersect(fileA,fileB,outfile,fraction,reciprocal)
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58 # number of overlaps
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59 nOverlapReal = lineCount(outfile)
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60
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61 print 'number of intervals in inputA that overlap with intervals in inputB:',nOverlapReal
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62
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63 # shuffle fileA to estimate background
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64 nOverlapNull = shuffle(fileA,fileB,genomefile,fraction,reciprocal,N)
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65
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66 # plot histogram
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67 rscript = open('tmp.r','w')
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68 rscript.write("x0 <- "+str(nOverlapReal)+"\n")
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69 rscript.write("x <- c("+','.join(map(str,nOverlapNull))+")\n")
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70 rscript.write("library(MASS)\n")
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71 rscript.write("\n")
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72 rscript.write("pv <- min((1+sum(x>=x0))/length(x),(1+sum(x<=x0))/length(x))\n")
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73 rscript.write("title <- paste('actual:chance = ',x0,':',round(mean(x)),' = ',format(x0/mean(x),digits=1,nsmall=2),', p-value < ',pv,sep='')\n")
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74 rscript.write("pdf('"+outplot+"')\n")
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75 rscript.write("h <- hist(x,breaks=50,xlab='number of overlaps',ylab='frequency',main=title)\n")
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76 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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77 rscript.write("points(x0,0,col='red')\n")
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78 rscript.write("dev.off()")
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79 rscript.close()
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80 os.system("R --vanilla < tmp.r")
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81 os.system('rm tmp.r')
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82 main()
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