R/app-psortb.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


ezMethodPsortb = function(input=NA, output=NA, param=NA, htmlFile="00index.html"){
  
  require(data.table)
  require(readr)
  require(dplyr)
  require(reshape2)
  require(tidyverse)
  
  opt = param$cmdOptions
  org = param$org
  sampleName = input$getNames()
  proteins = input$getFullPaths("Proteins")
  ezSystem(paste("mkdir", sampleName))
  cmd = paste("/usr/local/ngseq/src/psortb/psortb_app -i", proteins, "-r", sampleName, org, "--output terse", "-s /usr/local/ngseq/src/psortb/psortb.sif", opt, "1>", paste0(sampleName,"_psortb.log"))
  ezSystem(cmd)
  wddir <- "."
  outfile <- list.files(paste0(wddir, "/", sampleName), pattern="_psortb_.*\\.txt")
  outfile <- file.path(wddir, sampleName, outfile)
  ezSystem(paste("cp", outfile, basename(output$getColumn("PsortbOut"))))
  df = read_delim(outfile[1])
  list_of_OM_Ids = df[df$Localization == "OuterMembrane", c(1), drop = FALSE]
  write.table(sapply(str_split(list_of_OM_Ids$SeqID, " "), .subset ,1), paste0(wddir,"/", sampleName, "psortb.om.txt"), row.names = FALSE, quote=FALSE)
  cmd = paste("/usr/local/ngseq/packages/Tools/seqtk/1.4/bin/bin subseq", proteins, paste0(wddir,"/", sampleName, "psortb.om.txt"), ">", basename(output$getColumn("Proteins")))
  ezSystem(cmd)
  return("Success")

}


##' @template app-template
##' @templateVar method ezMethodPsortb
##' @description Use this reference class to run
EzAppPsortb <-
  setRefClass("EzAppPsortb",
              contains = "EzApp",
              methods = list(
                initialize = function() {
                  "Initializes the application using its specific defaults."
                  runMethod <<- ezMethodPsortb
                  name <<- "EzAppPsortb"
                  appDefaults <<- rbind(
                    org = ezFrame(Type="character",  DefaultValue="--negative",  Description="type of organism: gram negative/ gram positive bacteria or archea")
                  )
                }
              )
  )