From 1ac972542c47ffdda95a648d1b1e0c62ed5e3c5e Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Sun, 15 May 2016 22:14:35 +0200
Subject: [PATCH] Added basic testing
---
.../mapping/MultisampleMapping.scala | 5 +-
.../mapping/MultisampleMappingTest.scala | 133 ++++++++++++++++++
2 files changed, 135 insertions(+), 3 deletions(-)
create mode 100644 mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingTest.scala
diff --git a/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMapping.scala b/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMapping.scala
index f0d3c7313..4c039383a 100644
--- a/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMapping.scala
+++ b/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMapping.scala
@@ -43,7 +43,7 @@ trait MultisampleMappingTrait extends MultiSampleQScript
/** With this method the merge strategy for libraries to samples is defined. This can be overriden to fix the merge strategy. */
def mergeStrategy: MergeStrategy.Value = {
val value: String = config("merge_strategy", default = "preprocessmarkduplicates")
- MergeStrategy.values.find(_.toString.toLowerCase == value) match {
+ MergeStrategy.values.find(_.toString.toLowerCase == value.toLowerCase) match {
case Some(v) => v
case _ => throw new IllegalArgumentException(s"merge_strategy '$value' does not exist")
}
@@ -151,10 +151,9 @@ trait MultisampleMappingTrait extends MultiSampleQScript
try {
header.getSequenceDictionary.assertSameDictionary(referenceFile.getSequenceDictionary)
} catch {
- case e: AssertionError => {
+ case e: AssertionError =>
logger.error(e.getMessage)
oke = false
- }
}
oke
}
diff --git a/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingTest.scala b/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingTest.scala
new file mode 100644
index 000000000..f0449a7e0
--- /dev/null
+++ b/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingTest.scala
@@ -0,0 +1,133 @@
+package nl.lumc.sasc.biopet.pipelines.mapping
+
+import java.io.{File, FileOutputStream}
+
+import com.google.common.io.Files
+import nl.lumc.sasc.biopet.extensions.picard.{MarkDuplicates, MergeSamFiles}
+import nl.lumc.sasc.biopet.utils.ConfigUtils
+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 15/05/16.
+ */
+class MultisampleMappingTest extends TestNGSuite with Matchers {
+ def initPipeline(map: Map[String, Any]): MultisampleMapping = {
+ new MultisampleMapping() {
+ override def configNamespace = "multisamplemapping"
+ override def globalConfig = new Config(ConfigUtils.mergeMaps(map, MultisampleMappingTestTrait.config))
+ qSettings = new QSettings
+ qSettings.runName = "test"
+ }
+ }
+
+ def mergeStrategies = MultisampleMapping.MergeStrategy.values
+ def bamToFastq = false
+ def correctReadgroups = false
+
+ @DataProvider(name = "mappingOptions")
+ def mappingOptions = {
+ val bool = Array(true, false)
+ for (
+ merge <- mergeStrategies.toArray; sample2 <- bool
+ ) yield Array(merge, true, sample2)
+ }
+
+ @Test(dataProvider = "mappingOptions")
+ def testMultisampleMapping(merge: MultisampleMapping.MergeStrategy.Value, sample1: Boolean, sample2: Boolean): Unit = {
+ val map: Map[String, Any] = {
+ var m: Map[String, Any] = MultisampleMappingTestTrait.config
+ if (sample1) m = ConfigUtils.mergeMaps(MultisampleMappingTestTrait.sample1, m)
+ if (sample2) m = ConfigUtils.mergeMaps(MultisampleMappingTestTrait.sample2, m)
+ m ++ Map("merge_strategy" -> merge.toString, "bam_to_fastq" -> bamToFastq, "correct_readgroups" -> correctReadgroups)
+ }
+
+ if (!sample1 && !sample2) { // When no samples
+ intercept[IllegalArgumentException] {
+ initPipeline(map).script()
+ }
+ } 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)
+
+ import MultisampleMapping.MergeStrategy
+ pipeline.functions.count(_.isInstanceOf[MarkDuplicates]) shouldBe (numberLibs +
+ (if (sample2 && (merge == MergeStrategy.MarkDuplicates || merge == MergeStrategy.PreProcessMarkDuplicates)) 1 else 0))
+ pipeline.functions.count(_.isInstanceOf[MergeSamFiles]) shouldBe (
+ (if (sample2 && (merge == MergeStrategy.MergeSam || merge == MergeStrategy.PreProcessMergeSam)) 1 else 0))
+ pipeline.samples.foreach { case (sampleName, sample) =>
+ if (merge == MergeStrategy.None) sample.bamFile shouldBe None
+ }
+ }
+ }
+}
+
+object MultisampleMappingTestTrait {
+ val outputDir = Files.createTempDir()
+ outputDir.deleteOnExit()
+ new File(outputDir, "input").mkdirs()
+ def inputTouch(name: String): File = {
+ val file = new File(outputDir, "input" + File.separator + name).getAbsoluteFile
+ Files.touch(file)
+ file
+ }
+
+ 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"),
+ "fastqc" -> Map("exe" -> "test"),
+ "input_alleles" -> "test",
+ "fastqc" -> Map("exe" -> "test"),
+ "seqtk" -> Map("exe" -> "test"),
+ "sickle" -> Map("exe" -> "test"),
+ "cutadapt" -> Map("exe" -> "test"),
+ "bwa" -> Map("exe" -> "test"),
+ "samtools" -> Map("exe" -> "test"),
+ "igvtools" -> Map("exe" -> "test"),
+ "wigtobigwig" -> Map("exe" -> "test"),
+ "md5sum" -> Map("exe" -> "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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