PedigreeQscript testing

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/PedigreeQscript.scala

@@ -13,14 +13,14 @@ import scala.io.Source
  *
  * A multi-sample Qscript with additional Pedigree information.
  * Pedigrees follow the PED standard.
- * See: http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml for the format
+ * See: http://zzz.bwh.harvard.edu/plink/data.shtml#ped
  *
  * Pedigrees may be parsed from the sample config and/or a supplied PED file.
  */
 trait PedigreeQscript extends MultiSampleQScript { qscript: QScript =>
 
   /* Optionally parse from ped file */
-  def ped: Option[File] = None
+  def ped: Option[File] = config("ped_file", default = None)
 
   /* The merge stategy to use when we have both a ped file and sample tag information */
   def mergeStrategy: PedMergeStrategy.Value = PedMergeStrategy.Concatenate
@@ -28,14 +28,14 @@ trait PedigreeQscript extends MultiSampleQScript { qscript: QScript =>
   /**
    * Case class representing a PED samples
    * For the PED format, see:
-   * http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml
+   * http://zzz.bwh.harvard.edu/plink/data.shtml#ped
    * @param familyId family id
    * @param individualId individual id
    * @param paternalId Optional paternal id
    * @param maternalId Optional maternal id
    * @param gender gender
    * @param affectedPhenotype Optional boolean
-   * @param genotypeFields optional genotype fileds
+   * @param genotypeFields optional genotype fields
    */
   case class PedSample(familyId: String, individualId: String,
                        paternalId: Option[String],
@@ -57,7 +57,7 @@ trait PedigreeQscript extends MultiSampleQScript { qscript: QScript =>
    * @return List[PedSample]
    */
   def getIndexSamples: List[PedSample] = {
-    pedSamples.filter(x => x.affectedPhenotype)
+    pedSamples.filter(x => x.affectedPhenotype.contains(true))
   }
 
   /**
@@ -186,8 +186,11 @@ trait PedigreeQscript extends MultiSampleQScript { qscript: QScript =>
         }
         case _ => "0"
       }
-      val line: String = s"${p.familyId}\t${p.individualId}\t$paternalField\t$maternalField\t$genderField\t$affectedField\t" +
-        p.genotypeFields.mkString("\t")
+      val mainLine: String = s"${p.familyId}\t${p.individualId}\t$paternalField\t$maternalField\t$genderField\t$affectedField"
+      val line = if (p.genotypeFields.nonEmpty) {
+        mainLine + "\t" + p.genotypeFields.mkString("\t")
+      } else mainLine
+
       writer.write(line + "\n")
     }
     writer.close()

biopet-core/src/test/resources/full.ped

+fam01	sample1	sample2	sample3	2	0
+fam01	sample2	0	0	1	0
+fam01	sample3	0	0	2	0
+fam02	sample4	sample5	sample6	2	2
+fam02	sample5	0	0	1	1
+fam02	sample6	0	0	2	1

biopet-core/src/test/resources/trio.ped

+fam02	sample4	sample5	sample6	2	2
+fam02	sample5	0	0	1	1
+fam02	sample6	0	0	2	1

biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/PedigreeQScriptTest.scala

+package nl.lumc.sasc.biopet.core
+
+
+import java.io.File
+import java.nio.file.Paths
+
+import nl.lumc.sasc.biopet.core.MultiSampleQScript.Gender
+import nl.lumc.sasc.biopet.core.extensions.Md5sum
+import nl.lumc.sasc.biopet.utils.config.Config
+import nl.lumc.sasc.biopet.utils.{ConfigUtils, Logging}
+import org.broadinstitute.gatk.queue.{QScript, QSettings}
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+import scala.language.reflectiveCalls
+import scala.collection.mutable.ListBuffer
+import scala.io.Source
+
+/**
+  * Created by Sander Bollen on 11-4-17.
+  */
+class PedigreeQScriptTest extends TestNGSuite with Matchers {
+  import PedigreeQScriptTest._
+
+  @Test
+  def testConfigPedigree(): Unit = {
+    val script = PedigreeQScriptTest(sample1 :: sample2 :: sample3 :: Nil)
+    script.init()
+    script.biopetScript()
+
+    script.pedSamples.size shouldBe 3
+    script.pedSamples.map(_.individualId).contains("sample1") shouldBe true
+    script.pedSamples.map(_.individualId).contains("sample2") shouldBe true
+    script.pedSamples.map(_.individualId).contains("sample3") shouldBe true
+  }
+
+  @Test
+  def testGenderCorrect(): Unit = {
+    val script = PedigreeQScriptTest(sample2 :: Nil)
+    script.init()
+    script.biopetScript()
+
+    script.pedSamples.size shouldBe 1
+    script.pedSamples.head.gender shouldEqual Gender.Male
+
+    val script2 = PedigreeQScriptTest(sample3 :: Nil)
+    script2.init()
+    script2.biopetScript()
+
+    script2.pedSamples.size shouldBe 1
+    script2.pedSamples.head.gender shouldEqual Gender.Female
+  }
+
+  @Test
+  def testIsSingle(): Unit = {
+    val script = PedigreeQScriptTest(sample2 :: Nil)
+    script.init()
+    script.biopetScript()
+
+    script.isSingle shouldBe true
+  }
+
+  @Test
+  def testPedParsing(): Unit = {
+    val script = PedigreeQScriptTest(trioPed :: Nil)
+    script.init()
+    script.biopetScript()
+
+    script.pedSamples.size shouldBe 3
+    script.pedSamples.map(_.individualId).contains("sample4") shouldBe true
+    script.pedSamples.map(_.individualId).contains("sample5") shouldBe true
+    script.pedSamples.map(_.individualId).contains("sample6") shouldBe true
+  }
+
+  @Test
+  def testIsMother() = {
+    val script = PedigreeQScriptTest(trioPed :: Nil)
+    script.init()
+    script.biopetScript()
+
+    script.isMother(script.pedSamples.filter(_.individualId == "sample6").head) shouldBe true
+  }
+
+  @Test
+  def testIsFather() = {
+    val script = PedigreeQScriptTest(trioPed :: Nil)
+    script.init()
+    script.biopetScript()
+
+    script.isFather(script.pedSamples.filter(_.individualId == "sample5").head) shouldBe true
+  }
+
+  @Test
+  def testIsTrio() = {
+    val script = PedigreeQScriptTest(trioPed :: Nil)
+    script.init()
+    script.biopetScript()
+
+    script.isTrio shouldBe true
+
+    val script2 = PedigreeQScriptTest(sample1 :: sample2 :: sample3 :: Nil)
+    script2.init()
+    script2.biopetScript()
+
+    script2.isTrio shouldBe false
+  }
+
+  @Test
+  def testConcatenation() = {
+    val script = PedigreeQScriptTest(sample1 :: sample2 :: sample3 :: trioPed :: Nil)
+    script.init()
+    script.biopetScript()
+
+    script.pedSamples.size shouldBe 6
+    script.pedSamples.map(_.individualId).contains("sample1") shouldBe true
+    script.pedSamples.map(_.individualId).contains("sample2") shouldBe true
+    script.pedSamples.map(_.individualId).contains("sample3") shouldBe true
+    script.pedSamples.map(_.individualId).contains("sample4") shouldBe true
+    script.pedSamples.map(_.individualId).contains("sample5") shouldBe true
+    script.pedSamples.map(_.individualId).contains("sample6") shouldBe true
+  }
+
+  @Test
+  def testWritePedFile(): Unit = {
+    val script = PedigreeQScriptTest(sample1 :: sample2 :: sample3 :: trioPed :: Nil)
+    script.init()
+    script.biopetScript()
+
+    val tmpFile = File.createTempFile("test", ".ped")
+    tmpFile.deleteOnExit()
+    script.writeToPedFile(tmpFile)
+
+    val expectedLines = Source.fromFile(resourcePath("/full.ped")).getLines().toList.sorted
+    val writtenLines = Source.fromFile(tmpFile).getLines().toList.sorted
+
+    writtenLines shouldEqual expectedLines
+  }
+
+}
+
+object PedigreeQScriptTest {
+
+  private def resourcePath(p: String): String = {
+    Paths.get(getClass.getResource(p).toURI).toString
+  }
+
+
+  val sample1 = Map("samples" ->
+    Map("sample1" ->
+      Map("tags" ->
+        Map("gender" -> "female",
+          "father" -> "sample2",
+          "mother" -> "sample3",
+          "family" -> "fam01"
+        )
+      )
+    )
+  )
+
+  val sample2 = Map("samples" ->
+    Map("sample2" ->
+      Map("tags" ->
+        Map("gender" -> "male",
+          "family" -> "fam01"
+        )
+      )
+    )
+  )
+
+  val sample3 = Map("samples" ->
+    Map("sample3" ->
+      Map("tags" ->
+        Map("gender" -> "female",
+          "family" -> "fam01"
+        )
+      )
+    )
+  )
+
+  val trioPed = Map("ped_file" -> resourcePath("/trio.ped"))
+
+
+  def apply(configs: List[Map[String, Any]], only: List[String] = Nil) = {
+    new QScript with PedigreeQscript { qscript =>
+
+      qSettings = new QSettings()
+      qSettings.runName = "test"
+
+      override val onlySamples = only
+
+      var buffer = new ListBuffer[String]()
+
+      override def globalConfig = new Config(configs
+        .foldLeft(Map[String, Any]()) { case (a, b) => ConfigUtils.mergeMaps(a, b) })
+
+      val parent = null
+
+      def getLastLogMessage: String = {
+        Logging.errors.toList.last.getMessage
+      }
+
+      class Sample(id: String) extends AbstractSample(id) {
+        class Library(id: String) extends AbstractLibrary(id) {
+          /** Function that add library jobs */
+          protected def addJobs(): Unit = {
+            buffer += config("test")
+          }
+
+          /** Must return files to store into summary */
+          def summaryFiles: Map[String, File] = Map()
+
+          /** Must returns stats to store into summary */
+          def summaryStats = Map()
+        }
+
+        /**
+          * Factory method for Library class
+          * @param id SampleId
+          * @return Sample class
+          */
+        def makeLibrary(id: String): Library = new Library(id)
+
+        /** Function to add sample jobs */
+        protected def addJobs(): Unit = {
+          buffer += s"$sampleId"
+          addPerLibJobs()
+          add(new Md5sum(qscript))
+        }
+
+        /** Must return files to store into summary */
+        def summaryFiles: Map[String, File] = Map()
+
+        /** Must returns stats to store into summary */
+        def summaryStats = Map()
+      }
+
+      /**
+        * Method where the multisample jobs should be added, this will be executed only when running the -sample argument is not given.
+        */
+      def addMultiSampleJobs(): Unit = {
+        add(new Md5sum(qscript))
+      }
+
+      /**
+        * Factory method for Sample class
+        * @param id SampleId
+        * @return Sample class
+        */
+      def makeSample(id: String): Sample = new Sample(id)
+
+      /** Must return a map with used settings for this pipeline */
+      def summarySettings: Map[String, Any] = Map()
+
+      /** File to put in the summary for thie pipeline */
+      def summaryFiles: Map[String, File] = Map()
+
+      /** Name of summary output file */
+      def summaryFile: File = new File("./summary.json")
+
+      /** Init for pipeline */
+      def init(): Unit = {
+      }
+
+      /** Pipeline itself */
+      def biopetScript(): Unit = {
+        addSamplesJobs()
+        addSummaryJobs()
+      }
+    }
+  }
+}