library(Biostrings)
##generate standard counts
randomnumber<-sample(1:50,length(testfasta1),replace=TRUE)
standardcount<-data.frame(GeneID=names(testfasta1),stdcount=randomnumber)
write.table(standardcount,'standardcount',sep="\t")

##generate anchored reference
smallRNA<-readDNAStringSet("index.fa")
padseq<-function(x,adaptor5,adaptor3,subname){
  print(adaptor5)
  print(adaptor3)
  mmupad<-paste0(x,adaptor3)
  mmupad<-paste0(adaptor5,mmupad)
  mmupad<-DNAStringSet(mmupad)
  mmupad
  names(mmupad)<-gsub(" ","",names(x))
  names(mmupad)<-paste0(names(mmupad),subname)
  return(mmupad)
  
}
smallRNAanchored<- padseq(smallRNA,"CCCCCCCCCC","GGGGGGGGGG","")
writeXStringSet(smallRNAanchored,"smallRNAindexanchored.fa")
system("bowtie2-build smallRNAindexanchored.fa smallRNAindexanchored.fa")

##simulation data with anchor
testfasta1<-padseq(smallRNA,"CCCCCC","GGGGGG","")
standardcount<-read.table("standardcount",sep="\t")
sum(names(smallRNAanchored)!=standardcount$GeneID) #check sequence order
testfasta<-rep(testfasta1,standardcount$stdcount)
names(testfasta)<-c(1:length(testfasta))
writeXStringSet(testfasta,"testanchored.fa")

##simulation data without anchor
testfasta1<-padseq(smallRNA,"","","")
standardcount<-read.table("standardcount",sep="\t")
sum(names(smallRNAanchored)!=standardcount$GeneID) #check sequence order
testfasta<-rep(testfasta1,standardcount$stdcount)
names(testfasta)<-c(1:length(testfasta))
writeXStringSet(testfasta,"testfasta.fa")



##generate SAF shortstack index
sncRNA_SAF<-data.frame(GeneID=names(smallRNAanchored),Chr=names(smallRNAanchored),Start=1,End=width(smallRNAanchored),Strand="+")
write.table(sncRNA_SAF,"sncRNA_SAF.saf",quote=FALSE,sep="\t",row.names=FALSE)