R/app-samsa2.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


ezMethodSamsa2 = function(input=NA, output=NA, param=NA, 
                              htmlFile="00index.html"){
  ### metatranscriptomics assemby with Samsa2, annotation with RefSeq
  
  library(plyr)
  
  sampleName = input$getNames()
  file1PathInDatset <- input$getFullPaths("Read1")
  #fastqName1 <- paste0(sampleName,".R1.fastq")
  #cpCmd1 <- paste0("gunzip -c ", file1PathInDatset, "  > ", fastqName1)
  #ezSystem(cpCmd1)  
  if(param$paired){
    file2PathInDatset <- input$getFullPaths("Read2")
    #fastqName2 <- paste0(sampleName,".R2.fastq")
    #cpCmd2 <- paste0("gunzip -c ", file2PathInDatset, "  > ", fastqName2)
    #ezSystem(cpCmd2)
  } 
  ##make input directory
  make_inputDir <- paste("if [ -d input_files ]; then echo dir_exists; else mkdir input_files; fi")
  ezSystem(make_inputDir)
  move_input1 <- paste("cp", file1PathInDatset, "input_files")
  ezSystem(move_input1)
  if(param$paired){
    move_input2 <- paste("cp", file2PathInDatset, "input_files")
    ezSystem(move_input2)
  }
  ##copy samsa2
  cpSamsa2 <- paste("cp -r /usr/local/ngseq/src/samsa2/ .")
  ezSystem(cpSamsa2)
  #updateTemplateScriptCmd <- paste("cp",
  #                                 file.path(METAGENOMICS_ROOT,SAMSA2_TEMPLATE_SCRIPT),
  #                                  SAMSA2_TEMPLATE_SCRIPT)
  #ezSystem(updateTemplateScriptCmd)
  ## run bash script
  samsa2ToBeExecCmd <- paste("bash ./samsa2/bash_scripts/master_script.sh ./input_files/ .")
  ezSystem(samsa2ToBeExecCmd)
  
  ## place output files
  
  oldAnnFile <- list.files("step_4_output",pattern = "RefSeq_annotated",full.names = T)
  newAnnFile <- basename(output$getColumn("annotationFileRefSeq"))
  ezSystem(paste("mv",oldAnnFile,newAnnFile))
  oldAnnFile_org <- list.files("step_5_output/RefSeq_results/org_results",pattern = "RefSeq_annot",full.names = T)
  newAnnFile_org <- basename(output$getColumn("annotationORGFileRefSeq"))
  ezSystem(paste("mv",oldAnnFile_org,newAnnFile_org))
  oldAnnFile_func <- list.files("step_5_output/RefSeq_results/func_results",pattern = "RefSeq_annot",full.names = T)
  newAnnFile_func <- basename(output$getColumn("annotationFUNCFileRefSeq"))
  ezSystem(paste("mv",oldAnnFile_func,newAnnFile_func))
}

##' @template app-template
##' @templateVar method ezMethodSamsa2()
##' @templateVar htmlArg )
##' @description Use this reference class to run 
EzAppSamsa2 <-
  setRefClass("EzAppSamsa2",
              contains = "EzApp",
              methods = list(
                initialize = function()
                {
                  "Initializes the application using its specific defaults."
                  runMethod <<- ezMethodSamsa2
                  name <<- "EzAppSamsa2"
                  appDefaults <<- rbind(useSubsystemDB = ezFrame(Type="logical",
                                                                     DefaultValue="RefSeq",
                                                                     Description="database")
                                        
                                        
                  )
                }
              )
  )