R/systemTopHatBuild.R

In HenrikBengtsson/aroma.seq: High-Throughput Sequence Analysis using the Aroma Framework

###########################################################################/**
# @RdocDefault systemTopHatBuild
#
# @title "Calls the TopHat executable, specifically to build a transcriptome index"
#
# \description{
#  @get "title".
# }
#
# @synopsis
#
# \arguments{
#   \item{...}{Arguments specifying TopHat command line switches.}
#   \item{.fake}{If @TRUE, the executable is not called.}
#   \item{system2Args}{Arguments to be passed to system2}
#   \item{verbose}{See @see "R.utils::Verbose".}
# }
#
#
# @author "TT"
#
# @keyword internal
#*/###########################################################################
##
## - 20130215 This code will likely be superseded by systemTopHat.R; call that from a 'tophatBuild.R' (to be written)
##
setMethodS3("systemTopHatBuild", "default", function( ## ( No 'command' arg in this case )
                                                     ...,
                                                     system2Args,  ## explicitly split off arguments to be passed to system2
                                                     .fake=FALSE, verbose=FALSE) {
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Validate arguments
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

  # Arguments '...':
  args <- list(...) ## These are the arguments to *tophat*

  # Argument 'verbose':
  verbose <- Arguments$getVerbose(verbose)
  if (verbose) {
    pushState(verbose)
    on.exit(popState(verbose))
  }

  verbose && enter(verbose, "Calling TopHat executable")

  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Locate executable
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  bin <- findTopHat(verbose=less(verbose, 50))
  verbose && cat(verbose, "Executable:")
  verbose && print(verbose, bin)

  verbose && cat(verbose, "Arguments passed to system2():")
  verbose && str(verbose, system2Args)
  verbose && cat(verbose, "Arguments passed to TopHat:")
  verbose && str(verbose, args)

  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Setup command line switches
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

  ## args <- paste(keys, args, sep=" ")
  args <- trim(args)
  verbose && cat(verbose, "Command line options:")
  verbose && print(verbose, args)

  nms <- optionsList
  nms <- paste(ifelse(nchar(nms) == 1, "-", "--"), nms, sep="")
  names(optionsList) <- nms

  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # System call
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  verbose && cat(verbose, "System call:")
  cmd <- sprintf("%s %s", bin, paste(args, collapse=" "))
  verbose && print(verbose, cmd)
  verbose && str(verbose, system2Args)

  verbose && enter(verbose, "system2() call")
  callArgs <- list(command=bin, args=args)
  callArgs <- c(callArgs, system2Args)
  verbose && str(verbose, callArgs)
  if (!.fake) {
    res <- do.call(base::system2, callArgs)
  } else {
    res <- "<fake run>"
  }

  verbose && exit(verbose)
  verbose && exit(verbose)
  res
}) # systemTopHatBuild()