--- a/runproc.R	Wed Jan 31 14:13:11 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,105 +0,0 @@
-normdata<-function(case, control, method="nbinom")
-{	d=dnorm(-10:10,0,10);
-	u= c(rep(0,10),control,rep(0,10));
-	l=length(case);
-	nu=rep(0,l);
-	for(i in 1:21)
-	{	nu = nu + u[i-1+1:l] * d[i];
-	}
-	nu = nu / sum(d);
-
-	t = which(case<quantile(case,prob=0.99))
-	p=mean(case[t])/var(case[t]);
-	if(p>0.9) p=0.9;
-	if(p<0.1) p=0.1;
-	n=mean(case[t])*p/(1-p);
-	print(c(n,p));
-	#nc = log2((case*20+1)/(nu/mean(nu)*mean(case)*20+1)+1)-1;
-	if(method=="nbinom")
-	{	nc = -pnbinom(case,size=c((nu+1)/mean(nu+1)*n),prob=p,lower.tail=F,log.p=T)/log(10);
-	} else
-	{	nc = -ppois(case,(nu+1)/mean(nu+1)*mean(case),lower.tail=F,log.p=T)/log(10);
-	}
-	return(nc);
-}
-
-binsz=200
-folder="me66/Input/"
-mbed="/gpfs/group/yzz2/default/IDEAS_server/data/mm10.bed"
-
-#read file list
-args<-commandArgs(trailingOnly=TRUE);
-flist=args[1];
-x=as.matrix(read.table(flist));
-if(length(args) > 1)
-{	st=as.integer(args[2]);
-	ed=as.integer(args[3]);
-} else
-{	st=1;
-	ed=dim(x)[1];
-}
-l=paste(x[,1],x[,2]);
-ll=unique(l);
-id=rep(0,length(l));
-for(i in ll)
-{	t=which(l==i);
-	if(length(t)>1)
-	{	id[t]=1:length(t);
-	}
-}
-
-y=x[st:ed,1:3];
-if(dim(x)[2]==4)
-{ y=rbind(y,x[st:ed,c(1:2,4)]); }
-t=match(unique(y[,3]),y[,3]);
-k=rapply(as.list(y[t,3]),function(z){tail(unlist(gregexpr("\\/",z)),n=1);});
-y=cbind(y[t,],substr(y[t,3],k+1,1000));
-
-#fetch data and process data to windows mean
-for(i in 1:dim(y)[1])
-{	fout = paste(folder, y[i,1],"_",y[i,2],"_",y[i,4],sep="");	
-	system(paste("wget -O",fout, y[i,3]));
-	tl = tail(unlist(gregexpr("\\.",fout)),n=1);
-	name = substr(fout,1,tl);
-	ftype = substr(fout, tl+1, 100000);
-	if(tolower(ftype) == "bam")
-	{	system(paste("samtools index", fout));
-		bw=paste(name,".bw",sep="");
-		system(paste("bamCoverage --bam",fout,"-o",bw,"--binSize", binsz));
-	} else
-	{	bw=fout;
-	}
-	bd=paste(name,".bed",sep="");
-	system(paste("/storage/home/yzz2/work/tools/bigWigAverageOverBed", bw, mbed, "stdout | cut -f5 >", bd));
-	system(paste("gzip -f",bd));
-	system(paste("rm ", name,".ba*",sep=""));
-	system(paste("rm ", name,".bw",sep=""));
-}
-
-#normalize data if inputs are available, and prepare data file list
-fname=NULL;
-for(i in st:ed)
-{	k=match(x[i,3],y[,3]);
-	f1=paste(folder,y[k,1],"_",y[k,2],"_",substr(y[k,4],1,nchar(y[k,4])-4),".bed.gz",sep="");
-	if(dim(x)[2]==4)
-	{	k=match(x[i,4],y[,3]);
-		f0=paste(folder,y[k,1],"_",y[k,2],"_",substr(y[k,4],1,nchar(y[k,4])-4),".bed.gz",sep="");
-		if(id[i]>0) 
-		{	nf=paste(folder,x[i,1],".",x[i,2],"_",id[i],".norm.bed",sep="");
-		} else
-		{	nf=paste(folder,x[i,1],".",x[i,2],".norm.bed",sep="");
-		}	
-		x1=as.matrix(read.table(f1));
-		x0=as.matrix(read.table(f0));
-		nx=normdata(x1,x0);
-		write.table(round(nx*100)/100,nf,quote=F,row.names=F,col.names=F);
-		system(paste("gzip -f",nf));
-		fname=rbind(fname,c(x[i,1:2],paste(nf,".gz",sep="")));
-	} else
-	{	nf=paste(fold,x[i,1],".",x[i,2],".bed.gz",sep="");
-		system(paste("mv", f1, nf));
-		fname=rbind(fname,c(x[i,1:2],nf));
-	}
-}
-
-write.table(fname,paste(folder,"tmp_",st,"_",ed,".input",sep=""),quote=F,row.names=F,col.names=F);