--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mytools/binnedAverage.py	Tue Mar 13 23:34:52 2012 -0400
@@ -0,0 +1,77 @@
+'''
+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:
+            print 'not found:\t',line
+            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 <- read.table('"+outfile+"',sep='\t')\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))