added parameter options

reformat_output.R

@@ -1,7 +1,8 @@
 #!/usr/bin/env Rscript
-## author afust NEU
-## reformat BestperQuery_Hits table to table with all information about one peak in one row
 
+## author afust
+## reformat BestperQuery_Hits table to table with all information about one peak in one row
+library(getopt)
 
 ## columns given with $3 should be unique and not be seprated by the delimiter
 ## with the aggregate function the same entries are sepereated by it, so this has to be adjusted
@@ -11,73 +12,92 @@
 	}
 	return(entry)
 }
-
 #Script gets arguments
-args <- commandArgs(TRUE)
-# argument the scipt gets
-# $1 file which should be reformatted
-# $2 key column
-# $3 columns that should be kept 
-# $4 delimiter
-# $5 #cores
-if(length(args)>=4 && length(args)<=5){
-	print(Sys.time())
-	# Process arguments
-	df.hits <- read.table(args[1], header=TRUE, comment.char="#", sep="\t",check.names=FALSE, stringsAsFactors = FALSE)
-	key <- as.character(args[2])
-	keep.cols <- unlist(sapply(unlist(strsplit(args[3],",")), function(t) eval(parse(text=t))))
-	delimiter <- as.character(args[4])
-	cols<- colnames(df.hits)
-	## create output
-	output <- dirname(normalizePath(args[1]))
-	filename <- strsplit(basename(args[1]),"[.]")[[1]][1]
-	filename <- paste0(filename,"_compact.txt")
-	output <- paste(output,filename,sep="/")
-	# if multiple cores are present, use them.
-	if(length(args)==5){
-		cores <- as.numeric(args[5])
-		library(snow)
-  		c <- makeSOCKcluster(rep("localhost",cores))
-  		## replace occurence of delimiter in data
-  		if(delimiter != ";"){
-			df.hits[] <- parLapply(c,df.hits, gsub, pattern=delimiter, replacement=";", fixed=TRUE)
-		} else {
-			df.hits[] <- parLapply(c,df.hits, gsub, pattern=delimiter, replacement=",", fixed=TRUE)
-		}
+# 0 flag
+# 1 mandatory parameter
+# 2 optional parameter
+options <- matrix(c(
+	'input', 'i', 1, 'character', 'file which should be reformatted',
+	'key', 'k', 1, 'character', 'key columns seperated by "," without spaces',
+	'cols', 'c', 1, 'character', 'columns that should be kept ',
+	'delimiter', 'd', 2, 'character', 'delimiter [,]',
+	'threads', 't', 2, 'integer', 'cores to be used for reformatting',
+	'help', 'h', 0, 'logical','Provides command line help.'
+	), byrow=TRUE, ncol=5)
+opt <- getopt(options)
+#help
+if (!is.null(opt$help)) { 
+	cat(getopt(options, usage=TRUE))
+	q(status=0) }
+#check for mandatory input
+if (is.null(opt$input) || !file.exists(opt$input)) { 
+	cat("\nInput file to reformat is missing or not existend\n")
+	q(status=1) 
+}
+if (is.null(opt$key)) { 
+	cat("\nKey column is missing\n")
+	q(status=1)
+}
+if (is.null(opt$cols)) { 
+	cat("\nColumns to keep are missing\n")
+	q(status=1) 
+}
+#set defaults
+if (is.null(opt$delimiter)) { opt$delimiter <- "," }
+if (is.null(opt$threads)) { opt$threads <- 1 }
 
+# Process parameter
+df.hits <- read.table(opt$input, header=TRUE, comment.char="#", sep="\t",check.names=FALSE, stringsAsFactors = FALSE)
+cols <- colnames(df.hits)
+key <- as.character(opt$key)
+keep.cols <- unlist(sapply(unlist(strsplit(opt$cols,",")), function(t) eval(parse(text=t))))
+delimiter <- as.character(opt$delimiter)
+
+## create output
+output <- dirname(normalizePath(opt$input))
+filename <- strsplit(basename(opt$input),"[.]")[[1]][1]
+filename <- paste0(filename,"_compact.txt")
+output <- paste(output,filename,sep="/")
+# if multiple cores are present, use them.
+if(opt$threads > 1){
+	cores <- as.numeric(opt$threads)
+	library(snow)
+  	c <- makeSOCKcluster(rep("localhost",cores))
+  	## replace occurence of delimiter in data
+  	if(delimiter != ";"){
+		df.hits[] <- parLapply(c,df.hits, gsub, pattern=delimiter, replacement=";", fixed=TRUE)
 	} else {
-		## replace occurence of delimiter in data
-		if(delimiter != ";"){
-			df.hits[] <- lapply(df.hits, gsub, pattern=delimiter, replacement=";", fixed=TRUE)
-		} else {
-			df.hits[] <- lapply(df.hits, gsub, pattern=delimiter, replacement=",", fixed=TRUE)
-		}
+		df.hits[] <- parLapply(c,df.hits, gsub, pattern=delimiter, replacement=",", fixed=TRUE)
+	}
+} else {
+	## replace occurence of delimiter in data
+	if(delimiter != ";"){
+		df.hits[] <- lapply(df.hits, gsub, pattern=delimiter, replacement=";", fixed=TRUE)
+	} else {
+		df.hits[] <- lapply(df.hits, gsub, pattern=delimiter, replacement=",", fixed=TRUE)
 	}
-	# combind data by key column
-	df.reformat <- aggregate(.~df.hits[,key], data=df.hits, FUN=paste, collapse=delimiter, na.action=na.pass)
-	# remove key column and replace by aggregated column
-	df.reformat[,key] <- NULL
-	cols.new <- colnames(df.reformat)
-	cols.new[1] <- key
-	colnames(df.reformat) <- cols.new
-	#original column order
-	df.reformat <- df.reformat[,cols]
-	# transform columns that should be kept
-	for(i in 1:length(cols[keep.cols])){
-		if(length(args)==5){
-			col.unique <- parLapply(c, df.reformat[,keep.cols[i]], .reformat.keep.cols, delimiter)
-			df.reformat[,keep.cols[i]] <- unlist(col.unique)
-			if(i==length(cols[keep.cols])){
-				stopCluster(c)
-			}
-		} else {
-			col.unique <- lapply(df.reformat[,keep.cols[i]], .reformat.keep.cols, delimiter)
-			df.reformat[,keep.cols[i]] <- unlist(col.unique)
+}
+# combind data by key column
+df.reformat <- aggregate(.~df.hits[,key], data=df.hits, FUN=paste, collapse=delimiter, na.action=na.pass)
+# remove key column and replace by aggregated column
+df.reformat[,key] <- NULL
+cols.new <- colnames(df.reformat)
+cols.new[1] <- key
+colnames(df.reformat) <- cols.new
+#original column order
+df.reformat <- df.reformat[,cols]
+# transform columns that should be kept
+for(i in 1:length(cols[keep.cols])){
+	if(opt$threads > 1){
+		col.unique <- parLapply(c, df.reformat[,keep.cols[i]], .reformat.keep.cols, delimiter)
+		df.reformat[,keep.cols[i]] <- unlist(col.unique)
+		if(i==length(cols[keep.cols])){
+			stopCluster(c)
 		}
-
+	} else {
+		col.unique <- lapply(df.reformat[,keep.cols[i]], .reformat.keep.cols, delimiter)
+		df.reformat[,keep.cols[i]] <- unlist(col.unique)
 	}
-	#write to file
- 	write.table(df.reformat, output, append =FALSE, quote=FALSE,sep='\t', eol='\n',row.names = FALSE, col.names = TRUE)
- } else {
- 	cat("ERROR	wrong usage of script, use like this:\nRscript reformat.R <input> <key> <keep.cols> <delimiter> <<#threads>>\n\nFor example: Rscript reformat.R besthits.txt peak_id 1:3,5 ',' 5\nOr: Rscript reformat.R besthits.txt peak_id 1,3,5 '#'\nLast argument is optional, a number of threads can be added.\n")
- }
+}
+#write to file
+write.table(df.reformat, output, append =FALSE, quote=FALSE,sep='\t', eol='\n',row.names = FALSE, col.names = TRUE)