In Gaura/bioSeqGen: An R package to generate reads an anlyse associated data

set.seed(123)
startPos <- sample(1e6,nreads)
reads <- NULL
for(i in 1:nreads){
      if(startPos[i] + 9999 > 1e6){
            reads <- c(reads,substr(ecoli1M,startPos[i],1e6))
      }
      else{
            reads <- c(reads,substr(ecoli1M,startPos[i],startPos[i] + 9999))
      }

}

error = 0.1
nucleotides <- c('a','t','c','g')

flipReads <- function(rds,error){
flippedReads <- NULL
for(i in seq(1,length(rds))){
subread <- rds[i]
subreadLen <- nchar(subread)
nErrors <- floor(subreadLen * error)
subread <- strsplit(subread,'')[[1]]
subread <- flipBase(subread,subreadLen,nErrors)
flippedReads <- c(flippedReads, paste0(subread,collapse = ''))
}
return(flippedReads)
}

flipBase <- function(read,readLen,nErr){
samp <- sample(readLen,nErr)
for(i in 1:length(samp)){
      basePos <- which(nucleotides == read[samp[i]])
      read[samp[i]] <- sample(nucleotides[-basePos],1)
}
return(read)
}

read.fasta('data/ecoliGenome.fasta') -> ecoliSeq
ecoliSeq
ecoliSeq$NC_011750.1
View(ecoliSeq)
paste0(ecoliSeq$NC_011750.1)
paste0(ecoliSeq$NC_011750.1,collapse = '') -> ecoliGenome
nchars(ecoliGenome)
length(ecoliGenome)
ecoliGenome <- ecoliGenome[1]
length(ecoliGenome)
nchars(ecoliGenome)
nchar(ecoliGenome)
ecoli1M <- substr(ecoliGenome,1,1e6)