tests/testthat/test_apps-transcriptome-mapping.R

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

context("Mapping apps with example data")

## this tests do take long therefore we only run them if the environment variable RUN_LONG_TEST is set to TRUE
# Sys.setenv(RUN_LONG_TEST=TRUE)

cwd = getwd()

skipLong = function(){
  if (Sys.getenv("RUN_LONG_TEST") == "TRUE"){
    return()
  } else {
    skip("not running lengthy tests")
  }
}

yeastCommonMapParam = function(){
  param = list()
  param[['cores']] = '8'
  param[['ram']] = '20'
  param[['scratch']] = '100'
  param[['node']] = ''
  param[['process_mode']] = 'SAMPLE'
  param[['refBuild']] = 'Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Version-2013-03-07'
  param[['paired']] = 'true'
  param[['cmdOptions']] = ''
  param[['strandMode']] = 'sense'
  param[['refFeatureFile']] = 'genes.gtf'
  param[['trimAdapter']] = 'false'
  param[['trimLeft']] = '0'
  param[['trimRight']] = '0'
  param[['minTailQuality']] = '0'
  param[['specialOptions']] = ''
  param[['mail']] = ''
  param[['dataRoot']] = system.file(package="ezRun", mustWork = TRUE)
  param[['resultDir']] = 'p1001/Map_Result'
  return(param)
}


test_that("Map_Bowtie2Transcriptome", {
  skipLong()
  ezSystem("rm -fr /scratch/test_bowtie2transcriptomeMapping/*")
  setwdNew("/scratch/test_bowtie2transcriptomeMapping")
  param = yeastCommonMapParam()
  input = EzDataset$new(file=system.file("extdata/yeast_10k/dataset.tsv", package="ezRun", mustWork = TRUE), dataRoot=param$dataRoot)
  output = EzDataset$new(file=system.file("extdata/yeast_10k_Bowtie2Transcriptome/dataset.tsv", package="ezRun", mustWork = TRUE),
                         dataRoot=param$dataRoot)
  param[['cmdOptions']] = '--no-unal'
  myApp = EzAppBowtie2Transcriptome$new()
  myApp$run(input=input$copy()$subset(1), output=output$copy()$subset(1), param=param)
  setwd(cwd)
})


test_that("Profiles_TranscriptCoverage", {
  skipLong()
  ezSystem("rm -fr /scratch/test_TranscriptCoverage/*")
  setwdNew("/scratch/test_TranscriptCoverage")
  param = yeastCommonMapParam()
  input = EzDataset$new(file=system.file("extdata/yeast_10k_Bowtie2Transcriptome/dataset.tsv", package="ezRun", mustWork = TRUE),
                        dataRoot=param$dataRoot)
  meta = input$meta
  meta$"Count [File]" = paste0(input$getNames(), ".txt")
  meta$"Profiles [File]" = paste0(input$getNames(), "-profiles.RData")
  output = EzDataset$new(meta=meta, dataRoot=param$dataRoot)
  param[['minReadLength']] = 35
  param[['maxReadLength']] = 37
  param[["paired"]] = FALSE
  param[["getCoverageByReadLength"]] = TRUE
  
  myApp = EzAppTranscriptCoverage$new()
  myApp$run(input=input$copy()$subset(1), output=output$copy()$subset(1), param=param)
  setwd(cwd)
})