BastyTest.scala 7.56 KB
Newer Older
Peter van 't Hof's avatar
Peter van 't Hof committed
1 2
package nl.lumc.sasc.biopet.pipelines.basty

Peter van 't Hof's avatar
Peter van 't Hof committed
3
import java.io.{ File, FileOutputStream }
Peter van 't Hof's avatar
Peter van 't Hof committed
4 5

import com.google.common.io.Files
Peter van 't Hof's avatar
Peter van 't Hof committed
6 7
import nl.lumc.sasc.biopet.extensions.{ Raxml, RunGubbins }
import nl.lumc.sasc.biopet.extensions.gatk.{ BaseRecalibrator, IndelRealigner, PrintReads, RealignerTargetCreator }
Peter van 't Hof's avatar
Peter van 't Hof committed
8
import nl.lumc.sasc.biopet.extensions.picard.MarkDuplicates
Peter van 't Hof's avatar
Peter van 't Hof committed
9 10
import nl.lumc.sasc.biopet.extensions.tools.{ BastyGenerateFasta, VcfStats }
import nl.lumc.sasc.biopet.utils.{ ConfigUtils, Logging }
Peter van 't Hof's avatar
Peter van 't Hof committed
11 12 13 14
import nl.lumc.sasc.biopet.utils.config.Config
import org.broadinstitute.gatk.queue.QSettings
import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite
Peter van 't Hof's avatar
Peter van 't Hof committed
15
import org.testng.annotations.{ DataProvider, Test }
Peter van 't Hof's avatar
Peter van 't Hof committed
16 17

/**
Peter van 't Hof's avatar
Peter van 't Hof committed
18 19
 * Created by pjvanthof on 27/09/16.
 */
Peter van 't Hof's avatar
Peter van 't Hof committed
20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43
class BastyTest extends TestNGSuite with Matchers {
  def initPipeline(map: Map[String, Any]): Basty = {
    new Basty() {
      override def configNamespace = "shiva"
      override def globalConfig = new Config(ConfigUtils.mergeMaps(map, BastyTest.config))
      qSettings = new QSettings
      qSettings.runName = "test"
    }
  }

  @DataProvider(name = "bastyOptions")
  def bastyOptions = {
    for (
      s1 <- sample1; s2 <- sample2
    ) yield Array("", s1, s2)
  }

  def sample1 = Array(false, true)
  def sample2 = Array(false, true)
  def realign = true
  def baseRecalibration = true
  def multisampleCalling: Boolean = true
  def sampleCalling = false
  def libraryCalling = false
Peter van 't Hof's avatar
Peter van 't Hof committed
44
  def dbsnp = false
Peter van 't Hof's avatar
Peter van 't Hof committed
45 46 47
  def svCalling = false
  def cnvCalling = false
  def annotation = false
Peter van 't Hof's avatar
Peter van 't Hof committed
48
  def bootRuns: Option[Int] = None
Peter van 't Hof's avatar
Peter van 't Hof committed
49 50 51 52 53 54 55

  @Test(dataProvider = "bastyOptions")
  def testBasty(f: String, sample1: Boolean, sample2: Boolean): Unit = {
    val map = {
      var m: Map[String, Any] = BastyTest.config
      if (sample1) m = ConfigUtils.mergeMaps(BastyTest.sample1, m)
      if (sample2) m = ConfigUtils.mergeMaps(BastyTest.sample2, m)
Peter van 't Hof's avatar
Peter van 't Hof committed
56
      if (dbsnp) m = ConfigUtils.mergeMaps(Map("dbsnp_vcf" -> "test.vcf.gz"), m)
Peter van 't Hof's avatar
Peter van 't Hof committed
57 58 59 60 61 62 63 64
      ConfigUtils.mergeMaps(Map(
        "multisample_variantcalling" -> multisampleCalling,
        "single_sample_variantcalling" -> sampleCalling,
        "library_variantcalling" -> libraryCalling,
        "use_indel_realigner" -> realign,
        "use_base_recalibration" -> baseRecalibration,
        "sv_calling" -> svCalling,
        "cnv_calling" -> cnvCalling,
Peter van 't Hof's avatar
Peter van 't Hof committed
65 66
        "annotation" -> annotation,
        "boot_runs" -> bootRuns), m)
Peter van 't Hof's avatar
Peter van 't Hof committed
67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89

    }

    if (!sample1 && !sample2) { // When no samples
      intercept[IllegalArgumentException] {
        initPipeline(map).script()
      }
      Logging.errors.clear()
    } else {
      val pipeline = initPipeline(map)
      pipeline.script()

      val numberLibs = (if (sample1) 1 else 0) + (if (sample2) 2 else 0)
      val numberSamples = (if (sample1) 1 else 0) + (if (sample2) 1 else 0)

      pipeline.functions.count(_.isInstanceOf[MarkDuplicates]) shouldBe (numberLibs + (if (sample2) 1 else 0))

      // Gatk preprocess
      pipeline.functions.count(_.isInstanceOf[IndelRealigner]) shouldBe (numberLibs * (if (realign) 1 else 0) + (if (sample2 && realign) 1 else 0))
      pipeline.functions.count(_.isInstanceOf[RealignerTargetCreator]) shouldBe (numberLibs * (if (realign) 1 else 0) + (if (sample2 && realign) 1 else 0))
      pipeline.functions.count(_.isInstanceOf[BaseRecalibrator]) shouldBe (if (dbsnp && baseRecalibration) (numberLibs * 2) else 0)
      pipeline.functions.count(_.isInstanceOf[PrintReads]) shouldBe (if (dbsnp && baseRecalibration) numberLibs else 0)

Peter van 't Hof's avatar
Peter van 't Hof committed
90
      pipeline.summarySettings.get("boot_runs") shouldBe Some(bootRuns.getOrElse(100))
Peter van 't Hof's avatar
Peter van 't Hof committed
91

92 93 94
      pipeline.summaryFile shouldBe new File(BastyTest.outputDir, "Basty.summary.json")
      pipeline.summaryFiles shouldBe Map()

Peter van 't Hof's avatar
Peter van 't Hof committed
95 96
      pipeline.samples foreach {
        case (sampleId, sample) =>
Peter van 't Hof's avatar
Peter van 't Hof committed
97 98 99 100 101 102 103 104
          sample.summarySettings shouldBe Map()
          sample.summaryFiles.get("variants_fasta") should not be None
          sample.summaryFiles.get("consensus_fasta") should not be None
          sample.summaryFiles.get("consensus_variants_fasta") should not be None
          sample.summaryFiles.get("snps_only_variants_fasta") should not be None
          sample.summaryFiles.get("snps_only_consensus_fasta") should not be None
          sample.summaryFiles.get("snps_only_consensus_variants_fasta") should not be None
          sample.summaryStats shouldBe Map()
Peter van 't Hof's avatar
Peter van 't Hof committed
105 106
          sample.libraries.foreach {
            case (libId, lib) =>
Peter van 't Hof's avatar
Peter van 't Hof committed
107 108 109
              lib.summarySettings shouldBe Map()
              lib.summaryFiles shouldBe Map()
              lib.summaryStats shouldBe Map()
Peter van 't Hof's avatar
Peter van 't Hof committed
110 111 112 113 114
          }
      }

      pipeline.functions.count(_.isInstanceOf[VcfStats]) shouldBe (
        (if (multisampleCalling) 2 else 0) +
Peter van 't Hof's avatar
Peter van 't Hof committed
115 116
        (if (sampleCalling) numberSamples * 2 else 0) +
        (if (libraryCalling) numberLibs * 2 else 0))
Peter van 't Hof's avatar
Peter van 't Hof committed
117 118 119 120

      pipeline.functions.count(_.isInstanceOf[BastyGenerateFasta]) shouldBe 2 + (2 * numberSamples)
      pipeline.functions.count(_.isInstanceOf[Raxml]) shouldBe (2 * (2 + bootRuns.getOrElse(100)))
      pipeline.functions.count(_.isInstanceOf[RunGubbins]) shouldBe 2
Peter van 't Hof's avatar
Peter van 't Hof committed
121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212
    }
  }
}

object BastyTest {
  val outputDir = Files.createTempDir()
  outputDir.deleteOnExit()
  new File(outputDir, "input").mkdirs()
  def inputTouch(name: String): String = {
    val file = new File(outputDir, "input" + File.separator + name)
    Files.touch(file)
    file.getAbsolutePath
  }

  private def copyFile(name: String): Unit = {
    val is = getClass.getResourceAsStream("/" + name)
    val os = new FileOutputStream(new File(outputDir, name))
    org.apache.commons.io.IOUtils.copy(is, os)
    os.close()
  }

  copyFile("ref.fa")
  copyFile("ref.dict")
  copyFile("ref.fa.fai")

  val config = Map(
    "name_prefix" -> "test",
    "cache" -> true,
    "dir" -> "test",
    "vep_script" -> "test",
    "output_dir" -> outputDir,
    "reference_fasta" -> (outputDir + File.separator + "ref.fa"),
    "gatk_jar" -> "test",
    "samtools" -> Map("exe" -> "test"),
    "bcftools" -> Map("exe" -> "test"),
    "fastqc" -> Map("exe" -> "test"),
    "input_alleles" -> "test",
    "variantcallers" -> "raw",
    "fastqc" -> Map("exe" -> "test"),
    "seqtk" -> Map("exe" -> "test"),
    "sickle" -> Map("exe" -> "test"),
    "cutadapt" -> Map("exe" -> "test"),
    "bwa" -> Map("exe" -> "test"),
    "samtools" -> Map("exe" -> "test"),
    "macs2" -> Map("exe" -> "test"),
    "igvtools" -> Map("exe" -> "test", "igvtools_jar" -> "test"),
    "wigtobigwig" -> Map("exe" -> "test"),
    "md5sum" -> Map("exe" -> "test"),
    "bgzip" -> Map("exe" -> "test"),
    "tabix" -> Map("exe" -> "test"),
    "breakdancerconfig" -> Map("exe" -> "test"),
    "breakdancercaller" -> Map("exe" -> "test"),
    "pindelconfig" -> Map("exe" -> "test"),
    "pindelcaller" -> Map("exe" -> "test"),
    "pindelvcf" -> Map("exe" -> "test"),
    "clever" -> Map("exe" -> "test"),
    "delly" -> Map("exe" -> "test"),
    "rungubbins" -> Map("exe" -> "test"),
    "raxml" -> Map("exe" -> "test"),
    "pysvtools" -> Map(
      "exe" -> "test",
      "exclusion_regions" -> "test",
      "translocations_only" -> false),
    "freec" -> Map(
      "exe" -> "test",
      "chrFiles" -> "test",
      "chrLenFile" -> "test"
    )
  )

  val sample1 = Map(
    "samples" -> Map("sample1" -> Map("libraries" -> Map(
      "lib1" -> Map(
        "R1" -> inputTouch("1_1_R1.fq"),
        "R2" -> inputTouch("1_1_R2.fq")
      )
    )
    )))

  val sample2 = Map(
    "samples" -> Map("sample3" -> Map("libraries" -> Map(
      "lib1" -> Map(
        "R1" -> inputTouch("2_1_R1.fq"),
        "R2" -> inputTouch("2_1_R2.fq")
      ),
      "lib2" -> Map(
        "R1" -> inputTouch("2_2_R1.fq"),
        "R2" -> inputTouch("2_2_R2.fq")
      )
    )
    )))
}