## ---- eval=FALSE---------------------------------------------------------
#  setwd('/media/Storage/Work/MinION/')

## ---- eval=FALSE---------------------------------------------------------
#  download.file(url='ftp://ftp.sra.ebi.ac.uk/vol1/ERA375/ERA375987/oxfordnanopore_native/H566_30_min_inc.tar.gz',
#                destfile = 'typhi.rep1.tar.gz')
#  download.file(url='ftp://ftp.sra.ebi.ac.uk/vol1/ERA375/ERA375685/oxfordnanopore_native/H566_ON_inc.tar.gz',
#                destfile = 'typhi.rep2.tar.gz')
#  download.file(url='ftp://ftp.sra.ebi.ac.uk/vol1/ERA376/ERA376255/oxfordnanopore_native/raw_2_rabsch_R7.tar.gz',
#                destfile = 'typhi.rep3.tar.gz')

## ---- eval=FALSE---------------------------------------------------------
#  files.1 <- untar('typhi.rep1.tar.gz', list = TRUE)
#  extract.1 <- grep(pattern = "/FMH.*\\.fast5", files.1)
#  untar('typhi.rep1.tar.gz', files = files.1[extract.1], tar='internal', exdir = 'typhi.rep1')

## ---- eval=FALSE---------------------------------------------------------
#  files.2 <- untar('typhi.rep2.tar.gz', list = TRUE)
#  extract.2 <- grep(pattern = "/FMH.*\\.fast5", files.2)
#  untar('typhi.rep2.tar.gz', files = files.2[extract.2], tar='internal', exdir = 'typhi.rep2')

## ---- eval=FALSE---------------------------------------------------------
#  untar('typhi.rep3.tar.gz', files = 'raw_2_rabsch_R7/data_by_channel/', exdir = 'typhi.rep3')

## ---- eval=FALSE---------------------------------------------------------
#  fast5.1 <- list.files(path = "typhi.rep1", pattern = "*.fast5$",
#                        full.names = TRUE, recursive = TRUE)
#  fast5.2 <- list.files(path = "typhi.rep2", pattern = "*.fast5$",
#                        full.names = TRUE, recursive = TRUE)
#  fast5.3 <- list.files(path = "typhi.rep3", pattern = "*.fast5$",
#                        full.names = TRUE, recursive = TRUE)

## ---- eval=FALSE---------------------------------------------------------
#  library(IONiseR)
#  s.typhi.rep1 <- readFast5Summary(files = fast5.1)
#  s.typhi.rep2 <- readFast5Summary(files = fast5.2)
#  s.typhi.rep3 <- readFast5Summary(files = fast5.3)

## ---- eval=FALSE---------------------------------------------------------
#  addPassFail <- function(summaryData) {
#      ## calculate the mean base quality score for 2D reads
#      meanBaseQuality <- alphabetScore(quality(fastq2D(summaryData))) / width(fastq2D(summaryData))
#      ## any greater than 9 is a PASS, less than is FAIL
#      passFail <- ifelse(meanBaseQuality > 9, yes = TRUE, no = FALSE)
#      ## match the PASS/FAIL status with an id
#      passFail <- data.table(baseCalled(summaryData) %>%
#                     filter(full_2D == TRUE, strand== "template") %>%
#                     select(id), pass = passFail)
#      ## create FALSE vector for all fast5 files, including those with no 2D
#      tmp <- rep(FALSE, length(summaryData))
#      ## use the id field to set PASS for appropriate reads
#      tmp[filter(passFail, pass==TRUE)[,id]] <- TRUE
#      ## update readInfo slot with extract column
#      summaryData@readInfo <- mutate(readInfo(summaryData), pass = tmp)
#      return(summaryData)
#  }
#  
#  s.typhi.rep1 <- addPassFail(s.typhi.rep1)
#  s.typhi.rep2 <- addPassFail(s.typhi.rep2)
#  s.typhi.rep3 <- addPassFail(s.typhi.rep3)

## ---- eval=FALSE---------------------------------------------------------
#  save(s.typhi.rep1, file = "styphi.rep1.rda")
#  save(s.typhi.rep2, file = "styphi.rep2.rda")
#  save(s.typhi.rep3, file = "styphi.rep3.rda")