Mercurial > repos > xuebing > sharplabtool

comparison intersectSig.py @ 11:b7f1d9f8f3bc

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author xuebing
date Sat, 10 Mar 2012 07:59:27 -0500
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10:1558594a3c2e 11:b7f1d9f8f3bc
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()