Change the package path

R/import.ngsfilter.R

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+#' @include 02_class_metabarcoding.data.R
+NULL
+
+#' Read ngsfilter text file
+#' 
+#' Reads  the text file used for assigning reads to samples with the
+#'  \code{ngsfilter} command of the \strong{OBITools} package. 
+#' 
+#' @param file a string containing the file name for the \code{ngsfilter} command.
+#' @param platewell a string corresponding to the tag used for storing the sample location
+#'                  in the PCR plate. Should be of the form "nbPlate_Well" (e.g. "01_A02").
+#'                  Default is \code{NULL}
+#' @return \code{\link{import.ngsfilter.data}} returns a \code{\link{data.frame}} instance
+#' 
+#' @examples
+#' \dontshow{# switch the working directory to the data package directory}
+#' \dontshow{setwd(system.file("extdata", package="ROBITools"))}
+#' 
+#' data(termes)
+#' 
+#' # reading the termes_ngsfilt.txt file
+#' termes.ngs=import.ngsfilter.data('termes_ngsfilt.txt', platewell="position")
+#' 
+#' # including ngsfilter data into termes data
+#' attr(termes, "samples") = termes.ngs[rownames(termes),]
+#' 
+#' colnames(termes$samples)
+#'   
+#' @seealso \code{\link{import.metabarcoding.data}} and \code{\link{read.obitab}} for other methods of data importation 
+#'
+#' @author Lucie Zinger
+#' @keywords DNA metabarcoding
+#' @export
+#' 
+import.ngsfilter.data = function(file, platewell=NULL) {
+  raw = read.table(file, sep="\t")
+  
+  #get samples names
+  names = raw[,2]
+  
+  #form first part of the output table (default ngsfilter text input)
+  out = raw[,-c(2,3,ncol(raw))]
+  colnames(out) = c("Experiment", "primerF", "primerR")
+
+  #add tags
+  out[,c("tagF", "tagR")] = do.call("rbind", strsplit(as.vector(raw[,3]), "\\:"))
+  
+  #collect nb and names of additionnal information
+  max.add = max(unlist(lapply(strsplit(gsub("^F @ ","", raw[, ncol(raw)]), "; "), length)))
+  names.add = unique(unlist(lapply(strsplit(unlist(strsplit(gsub("^F @ ","", raw[, ncol(raw)]), "; ")), "="), "[[",1)))
+  
+  #form table of additionnal info
+  form = lapply(strsplit(gsub("^F @ ","", raw[, ncol(raw)]), "; "), strsplit, "=")
+  additionnals = as.data.frame(do.call("rbind", lapply(form, function(y) {
+    val = rep(NA, , max.add)
+    names(val) = names.add
+    val[match(unlist(lapply(y, "[[", 1)), names(val))] = gsub(";", "",unlist(lapply(y, "[[", 2)))
+    val
+  })))
+  
+  #create PCR plate coordinates
+  if(!is.null(platewell)) {
+    form = strsplit(as.vector(additionnals[, platewell]), "_")
+    nbPlate = as.numeric(gsub("^0", "", unlist(lapply(form, "[[", 1))))
+    wellPlate = unlist(lapply(form, "[[", 2))
+    xPlate = as.numeric(gsub("[A-Z]", "", wellPlate))
+    yPlate = as.numeric(as.factor(gsub("[0-9]*", "", wellPlate))) + 8*nbPlate
+    
+    additionnals = additionnals[,-grep(platewell, colnames(additionnals))]
+    out = data.frame(out, additionnals, nbPlate, wellPlate, xPlate, yPlate)
+  }
+  else {
+    additionnals[,ncol(additionnals)] = gsub(";","", additionnals[,ncol(additionnals)])
+    out = data.frame(out, additionnals)
+  }
+
+  rownames(out) = names
+  return(out)
+}