Change the package path

R/read.ngsfilter.R

@@ -0,0 +1,56 @@
+#' @include 02_class_metabarcoding.data.R
+NULL
+
+#' Read an OBITools ngsfilter file
+#' 
+#' Reads a ngsfilter file as formatted for the OBITools. For now, needs to be tab delimited till the "F" column. 
+#' Any additionnal information needs to be space delimited.
+#' 
+#' @seealso \code{\link{import.metabarcoding.data}}
+#' @author Lucie Zinger
+#' @keywords data import
+#' @export
+#' 
+
+read.ngsfilter <- function(filename, decimal='.', as.is=!stringsAsFactors, stringsAsFactors = default.stringsAsFactors()) {
+	
+	t<-read.table(file=filename, header=F, sep="\t", as.is=T)
+	beg <- t[,1:5]
+	
+	colnames(beg) <- c('experiment','sample','tags','forward_primer','reverse_primer')
+	if (length(unique(beg$sample))==nrow(beg)) 
+		rownames(beg) <- beg$sample
+	end <- t[,c(2,6)]
+	
+	#F <- unlist(lapply(end$V6, function(x) strsplit(x,"@")[[1]][1]))
+	rawextras <- unlist(lapply(end$V6, function(x) strsplit(x,"@")[[1]][2]))
+	
+	rawextras <- lapply(rawextras, function(s) strsplit(s, '; ')[[1]])
+	rawextras <- lapply(rawextras, function(l) unlist(lapply(l, function(s) sub("^ +","",s))))
+	rawextras <- lapply(rawextras, function(l) unlist(lapply(l, function(s) sub(" +$","",s))))
+	
+	
+	rawextras <- lapply(rawextras, function(l) unlist(lapply(l, function(s) strsplit(s,"="))))
+	
+	
+	columnnames <- unique(unlist(lapply(rawextras, function(l) l[seq(1,length(l),2)])))
+	
+	m <- matrix(nrow=nrow(end), ncol=length(columnnames))
+	colnames(m) <- columnnames
+	m <- as.data.frame(m)    
+	
+	
+	#print(head(rawextras))
+	
+	
+	tt <- lapply(rawextras, function(l) list(l[seq(1,length(l),2)],l[seq(2,length(l),2)]))
+	invisible(lapply(1:length(tt), function(i){m[i,tt[[i]][[1]]] <<- tt[[i]][[2]]}))
+	
+	invisible(lapply(colnames(m), function(n) m[,n] <<- type.convert(m[,n], dec=decimal, as.is=as.is)))
+	
+	ngs = cbind(beg, m)
+	rownames(ngs) = ngs$sample
+	class(ngs)<-c('ngsfilter.data',class(ngs))
+	
+	return(ngs)
+}