testcode/test_import.R

In jaspwn/LucifR:

## Choose first file in data set to set working directory

initFile <- file.choose()

baseName <- dirname(initFile)

fileList <- list.files(baseName)

numFiles <- length(fileList)

## preallocate data.table

n <- 48 * numFiles
rawData <- data.table::data.table(readtime = character(n),
                                  plategroup = integer(n),
                                  well = integer(n),
                                  position = character(n),
                                  counttime = numeric(n),
                                  CPS = integer(n),
                                  fileListID = character(n),
                                  #time = .POSIXct(character(n)),
                                  time = double(n),
                                  temp = numeric(n),
                                  group = character(n))

import_file <- function(x, bN = baseName, rD = rawData, nF = numFiles) {

  # create file path and name for input file
  fileName <- paste(baseName, x, sep = "/")

  # read each plate individually and set column names
  rawPlate <- read.csv(file = fileName,
                       skip = 1,
                       header = TRUE,
                       col.names = c("readtime", "plategroup", "well", "position", "counttime", "CPS"),
                       row.names = NULL,
                       strip.white = TRUE,
                       blank.lines.skip = TRUE,
                       stringsAsFactors = FALSE)

  # coerce into data.table
  data <- data.table::data.table(rawPlate)

  # add fileList ID to data
  data.table::set(data, j = "fileListID",
                  value = x)

  # read in plate metadata to get plate start time and read temp
  metaDate <- pipe(paste("awk '/Plate Sequence/ {print $6,$7}'",
                         fileName, sep = " "))
  data.table::set(data, j = "time",
                  value = as.POSIXct(strptime(readLines(metaDate),
                                              format = "%d/%m/%Y %H:%M:%S")))
  close(metaDate)

  metaTemp <- pipe(paste("awk '/Plate Sequence/ {print $9}'",
                         fileName, sep = " "))
  data.table::set(data, j = "temp",
                  value = as.numeric(gsub("[A-Z]|[a-z]|:",
                                          "\\1",
                                          readLines(metaTemp))))
  close(metaTemp)

  fileID <- as.numeric(tools::file_ext(x))

  ifelse(fileID %in% seq(1, numFiles, 5),
         data.table::set(data, j = "group",
                         value = "plate01"),
         ifelse(fileID %in% seq(2, numFiles, 5),
                data.table::set(data, j = "group",
                                value = "plate02"),
                ifelse(fileID %in% seq(3, numFiles, 5),
                       data.table::set(data, j = "group",
                                       value = "plate03"),
                       ifelse(fileID %in% seq(4, numFiles, 5),
                              data.table::set(data, j = "group",
                                              value = "plate04"),
                              data.table::set(data, j = "group",
                                              value = "plate05")))))


  minrow <- (fileID*48)-47
  maxrow <- (fileID*48)

  rawData[minrow:maxrow, ] <<- data


  return(rawData)

  #if (exists("rawData")) {
  #  rawData <- rbind(rawData, data)
  #} else {
  #  rawData <- data
  #}
}

print(baseName)

sapply(fileList, import_file,
       bN = baseName,
       rD = rawData,
       nF = numFiles)

# for (i in 1:length(fileList)) {
#
#   # create file path and name for input file
#   fileName <- paste(baseName, fileList[i], sep = "/")
#
#   # read each plate individually and set column names
#   rawPlate <- read.csv(file = fileName,
#                        skip = 1,
#                        header = TRUE,
#                        col.names = c("readtime", "plategroup", "well", "position", "counttime", "CPS"),
#                        row.names = NULL,
#                        strip.white = TRUE,
#                        blank.lines.skip = TRUE,
#                        stringsAsFactors = FALSE)
#
#   # coerce into data.table
#   data <- data.table::data.table(rawPlate)
#
#   # add fileList ID to data
#   data.table::set(data, j = "fileListID",
#                   value = fileList[i])
#
#   # read in plate metadata to get plate start time and read temp
#   metaDate <- pipe(paste("awk '/Plate Sequence/ {print $6,$7}'",
#                          fileName, sep = " "))
#   data.table::set(data, j = "time",
#                   value = as.POSIXct(strptime(readLines(metaDate),
#                                               format = "%d/%m/%Y %H:%M:%S")))
#   close(metaDate)
#
#   metaTemp <- pipe(paste("awk '/Plate Sequence/ {print $9}'",
#                          fileName, sep = " "))
#   data.table::set(data, j = "temp",
#                   value = as.numeric(gsub("[A-Z]|[a-z]|:",
#                                           "\\1",
#                                           readLines(metaTemp))))
#   close(metaTemp)
#
#   fileID <- as.numeric(tools::file_ext(fileList[i]))
#
#   ifelse(fileID %in% seq(1, length(fileList), 5),
#          data.table::set(data, j = "group",
#                          value = "plate01"),
#          ifelse(fileID %in% seq(2, length(fileList), 5),
#                 data.table::set(data, j = "group",
#                                 value = "plate02"),
#                 ifelse(fileID %in% seq(3, length(fileList), 5),
#                        data.table::set(data, j = "group",
#                                        value = "plate03"),
#                        ifelse(fileID %in% seq(4, length(fileList), 5),
#                               data.table::set(data, j = "group",
#                                               value = "plate04"),
#                               data.table::set(data, j = "group",
#                                               value = "plate05")))))
#
#
#   minrow <- (i*48)-47
#   maxrow <- (i*48)
#
#   rawData[minrow:maxrow, ] <- data
#
#   #if (exists("rawData")) {
#   #  rawData <- rbind(rawData, data)
#   #} else {
#   #  rawData <- data
#   #}
#
# }