Added check for optparse to bed_to_fasta.R

bin/2.2_motif_estimation/bed_to_fasta.R

@@ -1,13 +1,13 @@
 #!/usr/bin/env Rscript
-library("optparse")
+if (!require(optparse)) install.packages("optparse"); library(optparse)
 
 option_list <- list(
   make_option(opt_str = c("-i", "--input"), default = NULL, help = "Input bed-file. Second last column must be sequences and last column must be the cluster_id.", metavar = "character"),
   make_option(opt_str = c("-p", "--prefix"), default = "" , help = "Prefix for file names. Default = '%default'", metavar = "character"),
   make_option(opt_str = c("-m", "--min_seq"), default = 100, help = "Minimum amount of sequences in clusters. Default = %default", metavar = "integer")
 )
 
-opt_parser <- OptionParser(option_list = option_list, 
+opt_parser <- OptionParser(option_list = option_list,
                            description = "Convert BED-file to one FASTA-file per cluster")
 
 opt <- parse_args(opt_parser)
@@ -22,19 +22,19 @@ opt <- parse_args(opt_parser)
 #' @author René Wiegandt
 #' @contact rene.wiegandt(at)mpi-bn.mpg.de
 bed_to_fasta <- function(bedInput, prefix = "", min_seq = 100){
-  
+
   if (is.null(bedInput)) {
     stop("ERROR: Input parameter cannot be null! Please specify the input parameter.")
   }
 
   bed <- data.table::fread(bedInput, sep = "\t")
-  
+
   # Get last column of data.table, which refers to the cluster, as a vector.
   cluster_no <- as.vector(bed[[ncol(bed)]])
-  
+
   # Split data.table bed on its last column (cluster_no) into list of data.frames
   clusters <- split(bed, cluster_no, sorted = TRUE, flatten = FALSE)
-  
+
   # For each data.frame(cluster) in list clusters:
   discard <- lapply(1:length(clusters), function(i){
     clust <- as.data.frame(clusters[i])