Commit 3580cc2e authored by bow's avatar bow
Browse files

Merge branch 'feature-basty_testing' into 'develop'

Added testing to basty



See merge request !456
parents d43c8265 2d9ade1e
......@@ -54,5 +54,17 @@
<artifactId>Mapping</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.testng</groupId>
<artifactId>testng</artifactId>
<version>6.8</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.scalatest</groupId>
<artifactId>scalatest_2.10</artifactId>
<version>2.2.1</version>
<scope>test</scope>
</dependency>
</dependencies>
</project>
......@@ -33,10 +33,18 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
def this() = this(null)
case class FastaOutput(variants: File, consensus: File, consensusVariants: File)
case class FastaOutput(variants: File, consensus: File, consensusVariants: File) {
def summaryFiles(prefix: Option[String] = None) = Map(
s"${prefix.map(_ + "_").getOrElse("")}variants_fasta" -> variants,
s"${prefix.map(_ + "_").getOrElse("")}consensus_fasta" -> consensus,
s"${prefix.map(_ + "_").getOrElse("")}consensus_variants_fasta" -> consensusVariants
)
}
def variantcallers = List("unifiedgenotyper")
val numBoot = config("boot_runs", default = 100, namespace = "raxml").asInt
override def defaults = Map(
"ploidy" -> 1,
"variantcallers" -> variantcallers
......@@ -46,28 +54,26 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
def summaryFile: File = new File(outputDir, "Basty.summary.json")
//TODO: Add summary
def summaryFiles: Map[String, File] = Map()
//TODO: Add summary
def summarySettings: Map[String, Any] = Map()
def summarySettings: Map[String, Any] = Map("boot_runs" -> numBoot)
def makeSample(id: String) = new Sample(id)
class Sample(sampleId: String) extends AbstractSample(sampleId) {
//TODO: Add summary
def summaryFiles: Map[String, File] = Map()
def summaryFiles: Map[String, File] = output.summaryFiles() ++ outputSnps.summaryFiles(Some("snps_only"))
//TODO: Add summary
def summaryStats: Map[String, Any] = Map()
override def summarySettings: Map[String, Any] = Map()
def makeLibrary(id: String) = new Library(id)
class Library(libId: String) extends AbstractLibrary(libId) {
//TODO: Add summary
def summaryFiles: Map[String, File] = Map()
//TODO: Add summary
def summaryStats: Map[String, Any] = Map()
override def summarySettings: Map[String, Any] = Map()
protected def addJobs(): Unit = {}
}
......@@ -136,7 +142,6 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
add(raxmlMl)
val r = new scala.util.Random(seed)
val numBoot = config("boot_runs", default = 100, namespace = "raxml").asInt
val bootList = for (t <- 0 until numBoot) yield {
val raxmlBoot = new Raxml(this)
raxmlBoot.input = variants
......
@HD VN:1.4 SO:unsorted
@SQ SN:chr1 LN:9 UR:file:/home/pjvan_thof/pipelines/biopet/public/mapping/src/test/resources/ref.fa M5:fe15dbbd0900310caf32827f6da57550
package nl.lumc.sasc.biopet.pipelines.basty
import java.io.{ File, FileOutputStream }
import com.google.common.io.Files
import nl.lumc.sasc.biopet.extensions.{ Raxml, RunGubbins }
import nl.lumc.sasc.biopet.extensions.gatk.{ BaseRecalibrator, IndelRealigner, PrintReads, RealignerTargetCreator }
import nl.lumc.sasc.biopet.extensions.picard.MarkDuplicates
import nl.lumc.sasc.biopet.extensions.tools.{ BastyGenerateFasta, VcfStats }
import nl.lumc.sasc.biopet.utils.{ ConfigUtils, Logging }
import nl.lumc.sasc.biopet.utils.config.Config
import org.broadinstitute.gatk.queue.QSettings
import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite
import org.testng.annotations.{ DataProvider, Test }
/**
* Created by pjvanthof on 27/09/16.
*/
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
def dbsnp = false
def svCalling = false
def cnvCalling = false
def annotation = false
def bootRuns: Option[Int] = None
@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)
if (dbsnp) m = ConfigUtils.mergeMaps(Map("dbsnp" -> "test.vcf.gz"), m)
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,
"annotation" -> annotation,
"boot_runs" -> bootRuns), m)
}
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)
pipeline.summarySettings.get("boot_runs") shouldBe Some(bootRuns.getOrElse(100))
pipeline.summaryFile shouldBe new File(BastyTest.outputDir, "Basty.summary.json")
pipeline.summaryFiles shouldBe Map()
pipeline.samples foreach {
case (sampleId, sample) =>
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()
sample.libraries.foreach {
case (libId, lib) =>
lib.summarySettings shouldBe Map()
lib.summaryFiles shouldBe Map()
lib.summaryStats shouldBe Map()
}
}
pipeline.functions.count(_.isInstanceOf[VcfStats]) shouldBe (
(if (multisampleCalling) 2 else 0) +
(if (sampleCalling) numberSamples * 2 else 0) +
(if (libraryCalling) numberLibs * 2 else 0))
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
}
}
}
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")
)
)
)))
}
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