Mercurial > repos > xuebing > sharplabtool

comparison binnedAverage.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 get binned score of intervals,allow extension
3 '''
4
5 import os,sys,numpy,random,string
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,outfile,outplot,nbin):
25 '''
26 get binned average and std
27 '''
28 fbw = open(bwfile)
29 bw = BigWigFile(file=fbw)
30 fin = open(intvfile)
31 out = open(outfile,'w')
32 zeros = '\t'.join(['0']*nbin)
33 for line in fin:
34 #chrom,start,end,name,score,strand
35 line = line.strip()
36 flds = line.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 out.write(line+'\t'+zeros+'\n')
42 continue
43 # reverse if on minus strand
44 if flds[5] == '-':
45 scores = scores[::-1]
46 # no score = 0
47 scores = numpy.nan_to_num(scores)
48 # bin the data
49 binned = binning(scores,nbin)
50 out.write(line+'\t'+'\t'.join(map(str,binned))+'\n')
51 fin.close()
52 out.close()
53 # plot
54 if nbin > 1:
55 tmp = "".join(random.sample(string.letters+string.digits, 8))
56 rscript = open(tmp,"w")
57 rscript.write("options(warn=-1)\n")
58 rscript.write("x <- read.table('"+outfile+"',sep='\t')\n")
59 rscript.write("x <- x[,(ncol(x)+1-"+str(nbin)+"):ncol(x)]\n")
60 rscript.write("pdf('"+outplot+"')\n")
61 rscript.write("avg <- apply(x,2,mean)\n")
62 rscript.write("err <- apply(x,2,sd)/sqrt(nrow(x))\n")
63 rscript.write("print(avg)\n")
64 rscript.write("print(err)\n")
65 rscript.write("ylim=c(min(avg-err),max(avg+err))\n")
66 rscript.write("xticks <- seq(ncol(x))\n")
67 rscript.write("plot(xticks,avg,xlab='',ylab='average',type='l',lwd=0,ylim=ylim)\n")
68 rscript.write("polygon(c(xticks,rev(xticks)),c(avg+err,rev(avg-err)),col='lightgreen',border=NA)\n")
69 rscript.write("lines(xticks,avg,type='l',lwd=1)\n")
70 rscript.write("dev.off()\n")
71 rscript.close()
72 os.system("R --vanilla < "+tmp)
73 os.system("rm "+tmp)
74
75 print sys.argv
76 prog,bwfile,intvfile,nbin,outfile,outplot = sys.argv
77 getBinnedScore(bwfile,intvfile,outfile,outplot,int(nbin))