Added function to convert kraken to krona output

public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsKraken.scala

 package nl.lumc.sasc.biopet.pipelines.gears
 
+import java.io.{ File, PrintWriter }
+
 import nl.lumc.sasc.biopet.core.SampleLibraryTag
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
 import nl.lumc.sasc.biopet.extensions.kraken.{ KrakenReport, Kraken }
 import nl.lumc.sasc.biopet.extensions.tools.KrakenReportToJson
+import nl.lumc.sasc.biopet.utils.ConfigUtils
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.QScript
 
+import scala.collection.mutable
+import scala.xml.Node
+
 /**
  * Created by pjvanthof on 04/12/15.
  */
@@ -77,3 +83,55 @@ class GearsKraken(val root: Configurable) extends QScript with SummaryQScript wi
     case _          => Map()
   })
 }
+
+object GearsKraken {
+  def convertKrakenJsonToKronaXml(files: Map[String, File], outputFile: File): Unit = {
+
+    val oriMap = files.map { case (k, v) => k -> ConfigUtils.fileToConfigMap(v) }
+    val taxs: mutable.Map[String, Any] = mutable.Map()
+    def addTax(map: Map[String, Any], path: List[String] = Nil): Unit = {
+      val name = map("name").toString
+      val x = path.foldLeft(taxs)((a, b) => if (a.contains(b)) a(b).asInstanceOf[mutable.Map[String, Any]] else {
+        a += b -> mutable.Map[String, Any]()
+        a(b).asInstanceOf[mutable.Map[String, Any]]
+      })
+
+      if (!x.contains(name)) x += name -> mutable.Map[String, Any]()
+
+      map("children").asInstanceOf[List[Any]].foreach(x => addTax(x.asInstanceOf[Map[String, Any]], path ::: name :: Nil))
+    }
+    oriMap.foreach { x =>
+      addTax(x._2("classified").asInstanceOf[Map[String, Any]])
+    }
+
+    def getValue(sample: String, path: List[String], key: String) = {
+      path.foldLeft(oriMap(sample)("classified").asInstanceOf[Map[String, Any]]) { (b, a) =>
+        b.getOrElse("children", List[Map[String, Any]]())
+          .asInstanceOf[List[Map[String, Any]]]
+          .find(_.getOrElse("name", "") == a).getOrElse(Map[String, Any]())
+      }.get(key)
+    }
+
+    def createNodes(map: mutable.Map[String, Any], path: List[String] = Nil): Seq[Node] = {
+      (map.map {
+        case (k, v) =>
+          val node = <node name={ k }></node>
+          val sizes = oriMap.keySet.toList.map { sample => <val>{ getValue(sample, (path ::: k :: Nil).tail, "size").getOrElse(0) }</val> }
+          val size = <size>{ sizes }</size>
+          node.copy(child = size ++ createNodes(v.asInstanceOf[mutable.Map[String, Any]], path ::: k :: Nil))
+      }).toSeq
+    }
+    val xml = <krona>
+                <attributes magnitude="size">
+                  <attribute display="size">size</attribute>
+                </attributes>
+                <datasets>
+                  { oriMap.keySet.map { sample => <dataset>{ sample }</dataset> } }
+                </datasets>
+              </krona>
+
+    val writer = new PrintWriter(outputFile)
+    writer.println(xml.copy(child = xml.child ++ createNodes(taxs)).toString())
+    writer.close()
+  }
+}
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