Mercurial > repos > xuebing > sharplab_interval_analysis

comparison metaintv_ext.py @ 20:16ba480adf96

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author xuebing
date Sat, 31 Mar 2012 08:31:22 -0400
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19:d325683ec368 20:16ba480adf96
1 '''
2 get binned score of intervals,allow extension
3 '''
4
5 import os,sys,numpy
6 import string, random
7
8 from resize import *
9
10 from bx.bbi.bigwig_file import BigWigFile
11
12 def binning(x,n):
13 # make n bin of x
14 y = numpy.zeros(n,dtype=float)
15 if len(x) == 0:
16 return y
17 step = float(len(x))/n
18 for k in range(n):
19 i = int(step*k)
20 j = int(step*(k+1)) + 1
21 y[k] = x[i:j].mean()
22 #print i,j,k,y[k]
23 return y
24
25 def getBinnedScore(bwfile,intvfile,nbin):
26 '''
27 get binned average and std
28 '''
29 fbw = open(bwfile)
30 bw = BigWigFile(file=fbw)
31 fin = open(intvfile)
32 avg = numpy.zeros(nbin)
33 sqr = numpy.zeros(nbin)
34 N = 0
35 for line in fin:
36 #print N
37 #chrom,start,end,name,score,strand
38 flds = line.strip().split('\t')
39 #get the score at base resolution as an array
40 scores = bw.get_as_array(flds[0],int(flds[1]),int(flds[2]))
41 if scores == None:
42 print 'not found:\t',N,line
43 continue
44 N = N + 1
45 #print line,scores
46 # reverse if on minus strand
47 if flds[5] == '-':
48 scores = scores[::-1]
49 # no score = 0
50 scores = numpy.nan_to_num(scores)
51 # bin the data
52 binned = binning(scores,nbin)
53 avg = avg + binned
54 sqr = sqr + binned**2
55 # compute avg and std
56 avg = avg / N
57 err = ((sqr/N-avg**2)**0.5)/(N**0.5)
58 return avg,err,N
59
60 def getExtendedBinScore(bwfile,intvfile,nbins,exts):
61 '''
62 nbins: n1,n2,n3
63 exts: l1,l2,l3,l4
64 '''
65 avg = []
66 err = []
67 tmpfile = "".join(random.sample(string.letters+string.digits, 8))
68 if exts[0]>0 or exts[1]>0:
69 print 'make left extension'
70 resize(intvfile,tmpfile,'start-'+str(exts[0]),'start+'+str(exts[1]),'stranded')
71 print 'compute binned average'
72 avg,err,N = getBinnedScore(bwfile,tmpfile,nbins[0])
73 print 'regions used:',N
74 print 'make center region'
75 resize(intvfile,tmpfile,'start+'+str(exts[1]),'end-'+str(exts[2]),'stranded')
76 print 'compute binned average'
77 avg1,err1,N = getBinnedScore(bwfile,tmpfile,nbins[1])
78 print 'regions used:',N
79 avg = numpy.concatenate((avg,avg1))
80 err = numpy.concatenate((err,err1))
81 if exts[2]>0 or exts[3]>0:
82 print 'make right region'
83 resize(intvfile,tmpfile,'end-'+str(exts[2]),'end+'+str(exts[3]),'stranded')
84 print 'compute binned average'
85 avg2,err2,N = getBinnedScore(bwfile,tmpfile,nbins[2])
86 print 'regions used:',N
87 avg = numpy.concatenate((avg,avg2))
88 err = numpy.concatenate((err,err2))
89 os.system('rm '+tmpfile)
90 return avg,err
91
92 prog,bwfile,intvfile,exts,nbins,outfile,outplot = sys.argv
93 nbins = numpy.fromstring(nbins,dtype=int,sep=',')
94 exts = numpy.fromstring(exts,dtype=int,sep=',')
95 avg, err = getExtendedBinScore(bwfile,intvfile,nbins,exts)
96 print 'save data'
97 out = open(outfile,'w')
98 numpy.savetxt(out, avg, fmt='%.6f', delimiter=' ', newline=' ')
99 out.write('\n')
100 numpy.savetxt(out, err, fmt='%.6f', delimiter=' ', newline=' ')
101 out.write('\n')
102 out.close()
103
104 print 'plot'
105 start = exts[0]*nbins[0]/(exts[0]+exts[1])
106 end = nbins[0]+nbins[1]+exts[2]*nbins[2]/(exts[2]+exts[3])
107 #print start,end
108 rscript = open("tmp.r","w")
109 rscript.write("options(warn=-1)\n")
110 rscript.write("x <- read.table('"+outfile+"')\n")
111 rscript.write("pdf('"+outplot+"')\n")
112 rscript.write("avg <- x[1,]\n")
113 rscript.write("err <- x[2,]\n")
114 #rscript.write("print(x)\n")
115 rscript.write("ylim=c(min(avg-err),max(avg+err))\n")
116 rscript.write("xticks <- seq(ncol(x))\n")
117 #rscript.write("print(xticks)\n")
118 rscript.write("plot(xticks,avg,xlab='',ylab='average coverage',type='l',lwd=0,ylim=ylim,xaxt='n')\n")
119 rscript.write("axis(1, at=c(min(xticks),"+str(start)+","+str(end)+",max(xticks)),labels=c(-"+str(exts[0])+",0,0,"+str(exts[3])+"), las=2)\n")
120 rscript.write("polygon(c(xticks,rev(xticks)),c(avg+err,rev(avg-err)),col='lightgreen',border=NA)\n")
121 rscript.write("lines(xticks,avg,type='l',lwd=1)\n")
122 rscript.write("lines(c(min(xticks),max(xticks)),c(0,0),lwd=2)\n")
123 rscript.write("lines(c("+str(start)+","+str(end)+"),c(0,0),lwd=10)\n")
124 rscript.write("dev.off()\n")
125 rscript.close()
126 os.system("R --vanilla --slave < tmp.r")
127 os.system("rm tmp.r")
128