inst/extdata/PACVr_Rscript.R

In PACVr: Plastome Assembly Coverage Visualization

#!/usr/bin/R
#contributors = c("Michael Gruenstaeudl","Nils Jenke")
#email = "m.gruenstaeudl@fu-berlin.de", "nilsj24@zedat.fu-berlin.de"
#version = "2020.02.10.1300"

library("optparse")

########################################################################

CmdLineArgs <- function() {
  # Function to generate command line arguments
  # ARGS:---
  # RETURNS:
  #   user inputs 
  option_list <- list(
              # -g/i do not work due to R version bug
                  make_option(opt_str = c("-k","--gbkFile"), 
                              type    = "character", 
                              default = NULL, 
                              dest    = "gbkFile",
                              help    = "a text string that specifies the name of, and path to, the GenBank input file", 
                              metavar = "character"),
                  make_option(opt_str = c("-b","--bamFile"), 
                              type    = "character", 
                              default = NULL, 
                              dest    = "bamFile",
                              help    = "a text string that specifies the name of, and path to, the BAM input file", 
                              metavar = "character"),
                  make_option(opt_str = c("-w","--windowSize"), 
                              type    = "numeric", 
                              default = 250, 
                              dest    = "windowSize",
                              help    = "a numeric value that specifies window size in which the coverage is calculated [default = %default]", 
                              metavar = "integer"),
                  make_option(opt_str = c("-l","--logScale"), 
                              type    = "logical", 
                              default = FALSE, 
                              dest    = "logScale",
                              help    = "a boolean that specifies if the coverage depth is to be log-transformed before visualizing it [default = %default]", 
                              metavar = "logical"),
                  make_option(opt_str = c("-t","--threshold"), 
                              type    = "numeric", 
                              default = 0.5, 
                              dest    = "threshold",
                              help    = "a numeric value that specifies the threshold for plotting coverage depth bars in red as opposed to the default black [default = %default]", 
                              metavar = "integer"),
                  make_option(opt_str = c("-s","--syntenyLineType"), 
                              type    = "numeric", 
                              default = 1, 
                              dest    = "syntenyLineType",
                              help    = "a numeric value of 1, 2 or 3 that specifies the line type for visualizing IR gene synteny; 1 = ribbon lines, 2 = solid lines, 3 = no line [default = %default]", 
                              metavar = "integer"),
                  make_option(opt_str = c("-r","--relative"), 
                              type    = "logical", 
                              default = TRUE, 
                              dest    = "relative",
                              help    = "a boolean that specifies whether the threshold is a relative value of the average coverage instead of an absolute value [default = %default]", 
                              metavar = "logical"),
                  make_option(opt_str = c("-x","--textSize"), 
                              type    = "numeric", 
                              default = 0.5, 
                              dest    = "textSize",
                              help    = "a numeric value that specifies the relative font size of the text element in the visualization [default = %default]", 
                              metavar = "integer"),
                  make_option(opt_str = c("-d","--delete"), 
                              type    = "logical", 
                              default = TRUE, 
                              dest    = "delete",
                              help    = "the decision to delete temporary files upon program execution [default = %default]", 
                              metavar = "logical"),
                  make_option(opt_str = c("-o","--output"), 
                              type    = "character", 
                              default = "./PACVr_output.pdf", 
                              dest    = "output",
                              help    = "a text string that specifies the name of, and path to, the output file [default= %default]", 
                              metavar = "character"))
  
  opt_parse <- optparse::OptionParser(option_list=option_list)
  opt <- optparse::parse_args(opt_parse)
  if (is.null(opt$gbkFile)){
    print_help(opt_parse)
    warning("No .gb file supplied", call.=FALSE)
    stop("Error")
  }
  if (is.null(opt$bamFile)) {
    print_help(opt_parse)
    warning("No .bam file supplied", call.=FALSE)
    stop("Error")
  }
  return(opt)
}

opt <- CmdLineArgs()

########################################################################

require("PACVr")
PACVr.complete(gbk.file = opt$gbkFile,
               bam.file = opt$bamFile,
               windowSize = opt$windowSize,
               logScale = opt$logScale,
               threshold = opt$threshold,
               syntenyLineType = opt$syntenyLineType,
               relative = opt$relative,
               textSize = opt$textSize,
               delete = opt$delete,
               output = opt$output)

########################################################################