R/readPanelsFile.r

In strvalidator: Process Control and Validation of Forensic STR Kits

################################################################################
# TODO LIST
# TODO: Add support for several files in one go.

################################################################################
# CHANGE LOG (last 20 changes)
# 28.09.2015: Convert color names to lower case.
# 15.12.2014: Changed parameter names to format: lower.case
# 22.09.2013: Fixed bug when reading LifeTech bins with comment.
# 22.09.2013: Added 'debug' parameter.
# 22.06.2013: First version.

#' @title Read Panels File
#'
#' @description
#' Reads GeneMapper Panels files.
#'
#' @details Reads useful information from Panels files and save it as a data.frame.
#'
#' @param panel.files string, complete path to Panels file.
#' @param debug logical indicating printing debug information.
#'
#' @keywords internal
#'
#' @return data.frame containing the columns 'Panel', 'Marker', 'Color',
#' 'Marker.Min', 'Marker.Max', 'Repeat'.
#'

readPanelsFile <- function(panel.files, debug = FALSE) {
  # Constants.
  keyPanel <- "Panel"
  cDelimeter <- "\t"

  # Check if files are specified.
  if (!is.na(panel.files)) {
    # Open file for reading.
    f1 <- file(panel.files[1], open = "r")

    # Read raw text.
    allTextRaw <- readLines(f1)

    # Close file.
    close(f1)

    # Split text
    allTextSplit <- strsplit(allTextRaw, cDelimeter)

    # Create an empty data frame to hold the result.
    panels <- data.frame(t(rep(NA, 6)))
    # Add column names.
    names(panels) <- c(
      "Panel",
      "Marker",
      "Color",
      "Marker.Min",
      "Marker.Max",
      "Repeat"
    )
    # Remove all NAs
    panels <- panels[-1, ]

    # Get last index.
    rows <- length(allTextSplit)

    for (row in 1:rows) {
      currentTag <- allTextSplit[[row]][1]

      if (currentTag == keyPanel) {
        panelName <- allTextSplit[[row]][2]

        if (debug) {
          print("panelName")
          print(panelName)
        }

        # Read all lines until next panel or last row.
        repeat {
          # Repeat until found first marker row.
          # (This is for handle comments which is found in LifeTech files)
          repeat { #### BEGIN REPEAT!
            row <- row + 1
            if (row > rows) {
              break # Reached end of file.
            }
            currentTag <- allTextSplit[[row]][1]
            if (!grepl("#", currentTag, fixed = TRUE)) {
              break
            }
          } #### END REPEAT!

          if (row > rows) {
            if (debug) {
              print("END OF FILE!")
            }
            break # Reached end of file.
          }

          if (debug) {
            print("currentTag")
            print(currentTag)
          }

          if (currentTag == keyPanel) {
            break()
          }

          # Extract information.
          markerName <- allTextSplit[[row]][1]
          colorName <- tolower(allTextSplit[[row]][2])
          rangeMin <- as.numeric(allTextSplit[[row]][3])
          rangeMax <- as.numeric(allTextSplit[[row]][4])
          # [5] Positive control delimited by " # Not needed.
          repeatUnit <- as.numeric(allTextSplit[[row]][6])
          # [7] # ??? Not needed
          # allelicLadder <- allTextSplit[[row]][8] # Redundant (in bins).
          # Process allelic ladder string.
          # ladderTrim <- gsub("[[:space:]]", "", allelicLadder) # Removes all white spaces.
          # ladderTrim <- gsub("\"", "", ladderTrim) # Removes all white spaces.
          # alleleNames <- unlist(strsplit(ladderTrim,","))

          # Save information.
          currentMarker <- data.frame(
            Panel = panelName,
            Marker = markerName,
            Color = colorName,
            Marker.Min = rangeMin,
            Marker.Max = rangeMax,
            Repeat = repeatUnit,
            stringsAsFactors = FALSE
          )

          # Concatenate with data frame.
          panels <- rbind(panels, currentMarker)
        }
      }
    }

    return(panels)
  }
}