R/app-prodigal.R

In uzh/ezRun: An R meta-package for the analysis of Next Generation Sequencing Data

###################################################################
# Functional Genomics Center Zurich
# This code is distributed under the terms of the GNU General
# Public License Version 3, June 2007.
# The terms are available here: http://www.gnu.org/licenses/gpl.html
# www.fgcz.ch


ezMethodProdigal = function(input=NA, output=NA, param=NA, htmlFile="00index.html"){
  opt = param$cmdOptions
  sampleName = input$getNames()
  draft = input$getFullPaths("Draft")
  genes = paste0(sampleName,".genes")
  proteins = paste0(sampleName, ".proteins")
  cmd = paste("prodigal -i", draft, "-o", genes, "-a", proteins, "-f", param$format, "-g", param$translation_table, opt, "1>", paste0(sampleName,"_prodigal.log"))
  ezSystem(cmd)
  return("Success")
}


##' @template app-template
##' @templateVar method ezMethodProdigal
##' @description Use this reference class to run
##' @seealso \code{\link{getPbmm2Reference}}
EzAppProdigal <-
  setRefClass("EzAppProdigal",
              contains = "EzApp",
              methods = list(
                initialize = function() {
                  "Initializes the application using its specific defaults."
                  runMethod <<- ezMethodProdigal
                  name <<- "EzAppProdigal"
                  appDefaults <<- rbind(
                    translation_table = ezFrame(Type="integer",  DefaultValue="11",  Description="translation table to use (default 11)"),
                    format = ezFrame(Type="character", DefaultValue="gbk", Description="Select output format (gbk, gff, or sco).  Default is gbk.")
                  )
                }
              )
  )