### view tools/mytools/binnedAverage.py @ 1:cdcb0ce84a1b

author xuebing Fri, 09 Mar 2012 19:45:15 -0500 9071e359b9a3
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```
'''
get binned score of intervals,allow extension
'''

import os,sys,numpy,random,string

from resize import *

from bx.bbi.bigwig_file import BigWigFile

def binning(x,n):
# make n bin of x
y = numpy.zeros(n,dtype=float)
if len(x) == 0:
return y
step = float(len(x))/n
for k in range(n):
i = int(step*k)
j = int(step*(k+1)) + 1
y[k] = x[i:j].mean()
#print i,j,k,y[k]
return y

def getBinnedScore(bwfile,intvfile,outfile,outplot,nbin):
'''
get binned average and std
'''
fbw = open(bwfile)
bw = BigWigFile(file=fbw)
fin = open(intvfile)
out = open(outfile,'w')
zeros = '\t'.join(['0']*nbin)
for line in fin:
#chrom,start,end,name,score,strand
line = line.strip()
flds = line.split('\t')
#get the score at base resolution as an array
scores = bw.get_as_array(flds[0],int(flds[1]),int(flds[2]))
if scores == None:
out.write(line+'\t'+zeros+'\n')
continue
# reverse if on minus strand
if flds[5] == '-':
scores = scores[::-1]
# no score = 0
scores = numpy.nan_to_num(scores)
# bin the data
binned = binning(scores,nbin)
out.write(line+'\t'+'\t'.join(map(str,binned))+'\n')
fin.close()
out.close()
# plot
if nbin > 1:
tmp = "".join(random.sample(string.letters+string.digits, 8))
rscript = open(tmp,"w")
rscript.write("options(warn=-1)\n")
rscript.write("x <- x[,(ncol(x)+1-"+str(nbin)+"):ncol(x)]\n")
rscript.write("pdf('"+outplot+"')\n")
rscript.write("avg <- apply(x,2,mean)\n")
rscript.write("err <- apply(x,2,sd)/sqrt(nrow(x))\n")
rscript.write("print(avg)\n")
rscript.write("print(err)\n")
rscript.write("ylim=c(min(avg-err),max(avg+err))\n")
rscript.write("xticks <- seq(ncol(x))\n")
rscript.write("plot(xticks,avg,xlab='',ylab='average',type='l',lwd=0,ylim=ylim)\n")
rscript.write("polygon(c(xticks,rev(xticks)),c(avg+err,rev(avg-err)),col='lightgreen',border=NA)\n")
rscript.write("lines(xticks,avg,type='l',lwd=1)\n")
rscript.write("dev.off()\n")
rscript.close()
os.system("R --vanilla < "+tmp)
os.system("rm "+tmp)

print sys.argv
prog,bwfile,intvfile,nbin,outfile,outplot = sys.argv
getBinnedScore(bwfile,intvfile,outfile,outplot,int(nbin))
```