annotate mytools/binnedAverage.py @ 7:f0dc65e7f6c0

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author xuebing
date Fri, 09 Mar 2012 19:59:07 -0500
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7
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1 '''
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2 get binned score of intervals,allow extension
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3 '''
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4
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5 import os,sys,numpy,random,string
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6
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7 from resize import *
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8
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9 from bx.bbi.bigwig_file import BigWigFile
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10
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11 def binning(x,n):
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12 # make n bin of x
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13 y = numpy.zeros(n,dtype=float)
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14 if len(x) == 0:
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15 return y
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16 step = float(len(x))/n
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17 for k in range(n):
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18 i = int(step*k)
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19 j = int(step*(k+1)) + 1
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20 y[k] = x[i:j].mean()
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21 #print i,j,k,y[k]
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22 return y
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23
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24 def getBinnedScore(bwfile,intvfile,outfile,outplot,nbin):
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25 '''
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26 get binned average and std
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27 '''
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28 fbw = open(bwfile)
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29 bw = BigWigFile(file=fbw)
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30 fin = open(intvfile)
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31 out = open(outfile,'w')
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32 zeros = '\t'.join(['0']*nbin)
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33 for line in fin:
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34 #chrom,start,end,name,score,strand
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35 line = line.strip()
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36 flds = line.split('\t')
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37 #get the score at base resolution as an array
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38 scores = bw.get_as_array(flds[0],int(flds[1]),int(flds[2]))
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39 if scores == None:
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40 print 'not found:\t',line
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41 out.write(line+'\t'+zeros+'\n')
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42 continue
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43 # reverse if on minus strand
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44 if flds[5] == '-':
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45 scores = scores[::-1]
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46 # no score = 0
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47 scores = numpy.nan_to_num(scores)
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48 # bin the data
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49 binned = binning(scores,nbin)
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50 out.write(line+'\t'+'\t'.join(map(str,binned))+'\n')
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51 fin.close()
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52 out.close()
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53 # plot
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54 if nbin > 1:
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55 tmp = "".join(random.sample(string.letters+string.digits, 8))
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56 rscript = open(tmp,"w")
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57 rscript.write("options(warn=-1)\n")
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58 rscript.write("x <- read.table('"+outfile+"',sep='\t')\n")
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59 rscript.write("x <- x[,(ncol(x)+1-"+str(nbin)+"):ncol(x)]\n")
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60 rscript.write("pdf('"+outplot+"')\n")
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61 rscript.write("avg <- apply(x,2,mean)\n")
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62 rscript.write("err <- apply(x,2,sd)/sqrt(nrow(x))\n")
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63 rscript.write("print(avg)\n")
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64 rscript.write("print(err)\n")
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65 rscript.write("ylim=c(min(avg-err),max(avg+err))\n")
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66 rscript.write("xticks <- seq(ncol(x))\n")
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67 rscript.write("plot(xticks,avg,xlab='',ylab='average',type='l',lwd=0,ylim=ylim)\n")
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68 rscript.write("polygon(c(xticks,rev(xticks)),c(avg+err,rev(avg-err)),col='lightgreen',border=NA)\n")
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69 rscript.write("lines(xticks,avg,type='l',lwd=1)\n")
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70 rscript.write("dev.off()\n")
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71 rscript.close()
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72 os.system("R --vanilla < "+tmp)
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73 os.system("rm "+tmp)
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74
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75 print sys.argv
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76 prog,bwfile,intvfile,nbin,outfile,outplot = sys.argv
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77 getBinnedScore(bwfile,intvfile,outfile,outplot,int(nbin))