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comparison mytools/metaintv.py @ 9:87eb5c5ddfe9

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Uploaded
author xuebing
date Fri, 09 Mar 2012 20:01:43 -0500
parents f0dc65e7f6c0
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8:361ec1c0479d 9:87eb5c5ddfe9
1 '''
2 get binned score of intervals,allow extension
3 '''
4
5 import os,sys,numpy
6
7 from resize import *
8
9 from bx.bbi.bigwig_file import BigWigFile
10
11 def binning(x,n):
12 # make n bin of x
13 y = numpy.zeros(n,dtype=float)
14 if len(x) == 0:
15 return y
16 step = float(len(x))/n
17 for k in range(n):
18 i = int(step*k)
19 j = int(step*(k+1)) + 1
20 y[k] = x[i:j].mean()
21 #print i,j,k,y[k]
22 return y
23
24 def getBinnedScore(bwfile,intvfile,nbin):
25 '''
26 get binned average and std
27 '''
28 fbw = open(bwfile)
29 bw = BigWigFile(file=fbw)
30 fin = open(intvfile)
31 avg = numpy.zeros(nbin)
32 sqr = numpy.zeros(nbin)
33 N = 0
34 for line in fin:
35 #chrom,start,end,name,score,strand
36 flds = line.strip().split('\t')
37 #get the score at base resolution as an array
38 scores = bw.get_as_array(flds[0],int(flds[1]),int(flds[2]))
39 if scores == None:
40 print 'not found:\t',line
41 continue
42 N = N + 1
43 #print line,scores
44 # reverse if on minus strand
45 if flds[5] == '-':
46 scores = scores[::-1]
47 # no score = 0
48 scores = numpy.nan_to_num(scores)
49 # bin the data
50 binned = binning(scores,nbin)
51 avg = avg + binned
52 sqr = sqr + binned**2
53 # compute avg and std
54 avg = avg / N
55 err = ((sqr/N-avg**2)**0.5)/(N**0.5)
56 return avg,err
57
58 def getExtendedBinScore(bwfile,intvfile,nbins,exts):
59 '''
60 nbins: n1,n2,n3
61 exts: l1,l2,l3,l4
62 '''
63 # make left extension
64 resize(intvfile,intvfile+'.tmp','start-'+str(exts[0]),'start+'+str(exts[1]),'stranded')
65 # compute binned average
66 avg,err = getBinnedScore(bwfile,intvfile+'.tmp',nbins[0])
67 # make center region
68 resize(intvfile,intvfile+'.tmp','start+'+str(exts[1]),'end-'+str(exts[2]),'stranded')
69 # compute binned average
70 avg1,err1 = getBinnedScore(bwfile,intvfile+'.tmp',nbins[1])
71 avg = numpy.concatenate((avg,avg1))
72 err = numpy.concatenate((err,err1))
73 # make right region
74 resize(intvfile,intvfile+'.tmp','end-'+str(exts[2]),'end+'+str(exts[3]),'stranded')
75 # compute binned average
76 avg2,err2 = getBinnedScore(bwfile,intvfile+'.tmp',nbins[2])
77 avg = numpy.concatenate((avg,avg2))
78 err = numpy.concatenate((err,err2))
79
80 return avg,err
81
82 print sys.argv
83 prog,bwfile,intvfile,nbin,outfile,outplot = sys.argv
84 avg, err = getBinnedScore(bwfile,intvfile,int(nbin))
85 out = open(outfile,'w')
86 numpy.savetxt(out, avg, fmt='%.6f', delimiter=' ', newline=' ')
87 out.write('\n')
88 numpy.savetxt(out, err, fmt='%.6f', delimiter=' ', newline=' ')
89 out.write('\n')
90 out.close()
91
92 # plot
93 rscript = open("tmp.r","w")
94 rscript.write("options(warn=-1)\n")
95 rscript.write("x <- read.table('"+outfile+"')\n")
96 rscript.write("pdf('"+outplot+"')\n")
97 rscript.write("avg <- x[1,]\n")
98 rscript.write("err <- x[2,]\n")
99 rscript.write("print(x)\n")
100 rscript.write("ylim=c(min(avg-err),max(avg+err))\n")
101 rscript.write("xticks <- seq(ncol(x))\n")
102 rscript.write("plot(xticks,avg,xlab='',ylab='average coverage',type='l',lwd=0,ylim=ylim)\n")
103 rscript.write("polygon(c(xticks,rev(xticks)),c(avg+err,rev(avg-err)),col='lightgreen',border=NA)\n")
104 rscript.write("lines(xticks,avg,type='l',lwd=1)\n")
105 rscript.write("dev.off()\n")
106 rscript.close()
107 os.system("R --vanilla < tmp.r")
108 os.system("rm tmp.r")
109