R/systemBowtie2.R

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

###########################################################################/**
# @RdocDefault systemBowtie2
#
# @title "Wrapper for bowtie2"
#
# \description{
#  @get "title".
# }
#
# @synopsis
#
# \arguments{
#   \item{commandName}{A @character string specifying the bowtie2 command.}
#   \item{...}{Additional arguments specifying bowtie2 command line switches.}
#   \item{system2ArgsList}{Named list of arguments to pass to internal system2 call.}
#   \item{.fake}{If @TRUE, the executable is not called.}
#   \item{verbose}{See @see "R.utils::Verbose".}
# }
#
# @author "TT"
#
# @keyword internal
#*/###########################################################################
setMethodS3("systemBowtie2", "default", function(commandName="bowtie2",
                                                 ...,
                                                 system2ArgsList=list(stdout=TRUE, stderr=FALSE),
                                                 .fake=FALSE, verbose=FALSE
                                                 ) {
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Validate arguments
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Arguments '...':
  dotArgs <- list(...) ## list with one item named 'args'; these are the arguments to *bowtie2*

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

  verbose && enter(verbose, "Calling bowtie2 executable")

  ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Locate the bowtie2 executable
  bin <- findBowtie2(command=commandName, verbose=less(verbose, 50))
  verbose && cat(verbose, "Executable:")
  verbose && print(verbose, bin)
  verbose && cat(verbose, "Arguments passed to system2():")
  verbose && str(verbose, system2ArgsList)
  verbose && cat(verbose, "Arguments passed to bowtie2:")
  verbose && str(verbose, dotArgs)

  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Setup command line switches
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  verbose && cat(verbose, "Command line options:")
  verbose && print(verbose, dotArgs)

  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # System call
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  verbose && cat(verbose, "System call:")
  cmd <- sprintf("%s %s", bin, paste(dotArgs, collapse=" "))
  verbose && print(verbose, cmd)
  verbose && str(verbose, system2ArgsList)

  verbose && enter(verbose, "system2() call")
  callArgs <- list(command=bin, args=paste(names(dotArgs$args), dotArgs$args, sep=" "))
  callArgs <- c(callArgs, system2ArgsList)

  verbose && str(verbose, callArgs)
  if (!.fake) {
    res <- do.call(what=base::system2, args=callArgs)
  } else {
    cat("<fake run>\n")
    res <- "<fake run>"
  }

  verbose && exit(verbose)
  verbose && exit(verbose)
  res

  ## Strategy:  Previously, built up the command like this
  ##  cmdOptions <- .optionsList2String(optionsList)
  ##  cmdOptionsAdd <- .optionsList2String(list(...))
  ##  cmdOptions <- paste(cmdOptions, cmdOptionsAdd)
  ## Now assume the argument string is passed fully formed to systemBowtie2.

})