annotate interval/getGenomicScore.py @ 18:9bbb37e8683f

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import random,string,os,sys

    
def getScore(intvfile,outfile,summary_type,bwfilepath,nbin,strand,outplot,span):
    f = open(intvfile)
    tmpsh = "".join(random.sample(string.letters+string.digits, 8))
    tmpout = "".join(random.sample(string.letters+string.digits, 8))
    tmp = open(tmpsh,'w')
    if os.path.isdir(bwfilepath):
        for line in f:
            flds = line.strip().split('\t')
            cmd = 'bigWigSummary -type='+summary_type+' '+bwfilepath+'/'+flds[0]+'.bw '+flds[0]+' '+flds[1]+' '+flds[2]+' '+nbin+' >> '+tmpout+' 2>>'+tmpout+'\n'
            tmp.write(cmd)
    else:
        for line in f:
            flds = line.strip().split('\t')
            cmd = 'bigWigSummary -type='+summary_type+' '+bwfilepath+' '+flds[0]+' '+flds[1]+' '+flds[2]+' '+nbin+' >> '+tmpout+' 2>>'+tmpout+'\n'
            tmp.write(cmd)
    f.close()        
    # remove blank lines
    tmp.write("sed '/^$/d' "+tmpout+'>'+tmpout+".1\n")
    tmp.write("sed '/^Can/d' "+tmpout+".1 >"+tmpout+".2\n")
    # set n/a to 0
    tmp.write("sed 's/n\/a/0/g' "+tmpout+".2 >"+tmpout+".3\n")
    # replace text with 0
    zeros = ''.join(['0\t']*int(nbin))
    tmp.write("sed 's/^[a-zA-Z]/"+zeros+"/' "+tmpout+".3 >"+tmpout+".4\n")
    # cut the first nbin columns
    tmp.write("cut -f 1-"+nbin+" "+tmpout+".4 > "+tmpout+".5\n")     
    tmp.write("paste "+intvfile+" "+tmpout+".5 >"+outfile+"\n")
    tmp.close()
    os.system('chmod +x '+tmpsh)
    os.system('./'+tmpsh)
    #os.system('rm '+tmpout+'*')
    #os.system('rm '+tmpsh)

    # strandness: need to reverse bins for - strand
    if nbin > 1 and strand > 0:
        strand = strand - 1 # python is 0 based
        os.system('mv '+outfile+' '+tmpout)
        f = open(tmpout)
        out = open(outfile,'w')
        for line in f:
            flds=line.strip().split('\t')
            if flds[strand] == '+':
                out.write(line)
            else:
                scores = flds[-int(nbin):]
                scores.reverse()
                flds = flds[:-int(nbin)]+scores
                out.write('\t'.join(flds)+'\n')
        os.system('rm '+tmpout)
        f.close()
        out.close()
    # plot
    if int(nbin) > 1:
        rscript = open(tmpsh,"w")
        rscript.write("options(warn=-1)\n")
        rscript.write("x <- read.table('"+outfile+"',sep='\t')\n")
        rscript.write("x <- x[,(ncol(x)+1-"+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("ylim=c(min(avg-err),max(avg+err))\n")
        rscript.write("xticks <- seq(ncol(x))-(1+ncol(x))/2\n")
        if span >= 0.1:
            rscript.write("avg = loess(avg~xticks,span="+str(span)+")$fitted\n")
            rscript.write("err = loess(err~xticks,span="+str(span)+")$fitted\n")
        rscript.write("par(cex=1.5)\n")
        rscript.write("plot(xticks,avg,ylab='average conservation score',xlab='relative position (bin)',type='l',lwd=0,ylim=ylim)\n")   
        rscript.write("polygon(c(xticks,rev(xticks)),c(avg+err,rev(avg-err)),col='slateblue1',border=NA)\n")
        rscript.write("lines(xticks,avg,type='l',lwd=1)\n")   
        rscript.write("dev.off()\n")
        rscript.close()
        os.system("R --vanilla < "+tmpsh)
        os.system("rm "+tmpsh)

getScore(sys.argv[1],sys.argv[2],sys.argv[3],sys.argv[4],sys.argv[5],int(sys.argv[6]),sys.argv[7],float(sys.argv[8]))