Mercurial > repos > xuebing > sharplabtool

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