doSortedAnalysis.R

#!/software/R/3.0.2-gcc/bin/Rscript
# doSortedAnalysis.R : script for sorting stats data from multiple RAIDER_eval
#   output directories. Allows options for adding/removing/formatting data.
#   Arguments:
#     -v/--verbose  specifies whether output will print to stdout. default = True
#     -f/--fname    specifies stats file path
#     -o/--output   specifies file to print output to
#     --formula     specifies sorting formula for output. default = ~-tpr (Descending by sensitivity)
#     -a/--auto_out specifies to print output to default file in same directory
#     -t/--add_type specifies to add info about whether analyzing seq/sim data
#     -c/--add_chrom specifies to add info about chromosome being analyzed
#     -s/--suppress_seeds specifies not to add seed specific information
#     -i            specifies to not include time/space complexity information
#     -m            specifies to include directory information
# by Carly Schaeffer

suppressPackageStartupMessages(require(optparse))
source("sorted_analyze.R")

# specify our desired options
option_list = list(
  make_option(c("-v", "--verbose"), action="store_true", default=FALSE,
      help="Print extra output [default]"),
  make_option(c("-f", "--fname"), action="store", type="character", default=NA,
      help="Statistics file name"),
  make_option(c("-o", "--output"), type="character", default=NA,
      help="File to print output to"),
  make_option(c("--formula"), type="character", default="~-tpr",
      help = "Sorting formula [default \"%(default)s\"]"),
  make_option(c("-a", "--auto_out"), action="store_true", default=FALSE,
      help="Automatically create output file in same directory as stats file"),
  make_option(c("-t", "--add_type"), action="store_true", default=FALSE,
      help="Automatically add type info (sim vs seq_files)."),
  make_option(c("-c", "--add_chrom"), action="store_true", default=FALSE,
      help="Automatically add chrom info."),
  make_option(c("-s", "--suppress_seeds"), action="store_false", default=TRUE,
      help="Do not include seed info."),
  make_option(c("-i", "--suppress_complexity_info"), action="store_false", default=TRUE,
      help="Do not include info about time and space complexity"),
  make_option(c("-m", "--include_dir_info"), action="store_true", default=FALSE,
      help="Include directory name")
)

args = parse_args(OptionParser(option_list=option_list))


sortedAnalyze <- function(fname, verbose, output, form, auto_out, suppress_seeds, add_type, add_chrom, suppress_complexity_info, include_dir_info) {
  if(!is.na(fname)) {
    df <- addInfo(fname, suppress_seeds, add_type, add_chrom, include_dir_info) #getDf(fname)
    getSorted(df, verbose, output, form, auto_out, dirname(fname), suppress_complexity_info)
  } else {
    cat("Didn't specify file name\n", file=stderr()) # print error messages to stderr
  }
}

sortedAnalyze(args$fname, args$verbose, args$output, args$formula, args$auto_out, args$suppress_seeds, args$add_type, args$add_chrom, args$suppress_complexity_info, args$include_dir_info)