# R code

dir<-c("~/R/chongli/DMR_win/single_end/noiseout_window/")

head1<-paste(rep(c("5E","6D"),c(4,4)),c("5E","5A","5E","6B","6D","5A","6D","6B"),sep=".")
chr<-paste0(".chr",1:5)
sign<-c(".-",".+")
suffix<-c(".noiseout",".fdr0.05",".400")

for(n in 1:5){
  for(hi in c(1,3,5,7)){
    for(x in 0:1){
      filenames1<-paste0(dir[1],head1[hi],chr[n],sign[x+1],suffix[1]) 
      tmp1<-read.table(filenames1,header=T)

      filenames2<-paste0(dir[1],head1[hi+1],chr[n],sign[x+1],suffix[1])
      tmp2<-read.table(filenames2,header=T)

      results<-vector()
      long<-nrow(tmp1)

      for(j in 1:long){
           testmatrix<-rbind(tmp1[j,c(5,7)],tmp2[j,c(5,7)])
           fish<-fisher.test(testmatrix,alternative = "greater")
           results<-c(tmp1[j,1:2],x,fish$p.value)
        
           filename<-paste0(head1[hi+1],chr[n],sign[x+1],suffix[3])
           if(is.na(file.info(filename)[1])){
              names(results)<-c("start","end","strand","pvalue")
              write.table(t(results),file=filename,quote=F,row.names=F,sep="\t")
           }      
           else
              write.table(t(results),file=filename,append=T,quote=F,col.names=F,row.names=F,sep="\t")
      }
      
    } 
  }  
}