Fix markup in code

Reorganize output json, including unclassified readcount

public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/KrakenReportToJson.scala

@@ -21,13 +21,13 @@ class KrakenReportToJson(val root: Configurable) extends ToolCommandFuntion with
   def toolObject = nl.lumc.sasc.biopet.tools.KrakenReportToJson
 
   @Input(doc = "Input Kraken Full report", shortName = "inputReport", required = true)
-  var inputReport: File = null
+  var inputReport: File = _
 
   @Argument(required = false)
   var skipNames: Boolean = false
 
   @Output(doc = "Output JSON", shortName = "output", required = true)
-  var output: File = null
+  var output: File = _
 
   override def defaultCoreMemory = 1.0
 
@@ -37,9 +37,7 @@ class KrakenReportToJson(val root: Configurable) extends ToolCommandFuntion with
     conditional(skipNames, "--skipnames")
 
   def summaryStats: Map[String, Any] = {
-    val map = ConfigUtils.fileToConfigMap(output)
-
-    ConfigUtils.any2map(map.getOrElse("stats", Map()))
+    ConfigUtils.fileToConfigMap(output)
   }
 
   def summaryFiles: Map[String, File] = Map()

public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/KrakenReportToJson.scala

@@ -24,7 +24,7 @@ import java.io.{ PrintWriter, File }
 import nl.lumc.sasc.biopet.utils.ConfigUtils._
 import nl.lumc.sasc.biopet.utils.ToolCommand
 import scala.collection.mutable.ListBuffer
-import scala.collection.{ immutable, mutable }
+import scala.collection.mutable
 
 import scala.io.Source
 
@@ -36,8 +36,8 @@ case class KrakenHit(taxonomyID: Long,
                      cladeLevel: Int,
                      parentTaxonomyID: Long,
                      children: ListBuffer[KrakenHit]) {
-  def toJSON(): Map[String, Any] = {
-    val childJSON = children.toList.map(entry => entry.toJSON())
+  def toJSON(withChildren: Boolean = false): Map[String, Any] = {
+    val childJSON = if (withChildren) children.toList.map(entry => entry.toJSON(withChildren)) else List()
     Map(
       "name" -> taxonomyName,
       "taxid" -> taxonomyID,
@@ -55,6 +55,7 @@ object KrakenReportToJson extends ToolCommand {
 
   var cladeIDs: mutable.ArrayBuffer[Long] = mutable.ArrayBuffer.fill(32)(0)
   val spacePattern = "^( +)".r
+  private var lines: Map[Long, KrakenHit] = Map.empty
 
   case class Args(krakenreport: File = null, outputJson: Option[File] = None, skipNames: Boolean = false) extends AbstractArgs
 
@@ -132,7 +133,7 @@ object KrakenReportToJson extends ToolCommand {
     * 6. indented scientific name
     * */
 
-    val lines = reader.getLines()
+    lines = reader.getLines()
       .map(line => parseLine(line, skipNames))
       .filter(p => p.head._2.cladeSize > 0)
       .foldLeft(Map.empty[Long, KrakenHit])((a, b) => {
@@ -141,11 +142,22 @@ object KrakenReportToJson extends ToolCommand {
 
     lines.keys.foreach(k => {
       // append itself to the children attribute of the parent
-      lines(lines(k).parentTaxonomyID).children += lines(k)
+      if (lines(k).parentTaxonomyID > 0L) {
+        // avoid the root and unclassified appending to the unclassified node
+        lines(lines(k).parentTaxonomyID).children += lines(k)
+      }
     })
 
-    mapToJson(lines(1).toJSON()).spaces2
+    val result = Map("unclasified" -> lines(0).toJSON(withChildren = false),
+      "classified" -> lines(1).toJSON(withChildren = true))
+    mapToJson(result).spaces2
+
+  }
 
+  def summary: String = {
+    val result = Map("unclasified" -> lines(0).toJSON(withChildren = false),
+      "classified" -> lines(1).toJSON(withChildren = true))
+    mapToJson(result).spaces2
   }
 
   def main(args: Array[String]): Unit = {
@@ -153,11 +165,10 @@ object KrakenReportToJson extends ToolCommand {
 
     val jsonString: String = reportToJson(commandArgs.krakenreport, skipNames = commandArgs.skipNames)
     commandArgs.outputJson match {
-      case Some(file) => {
+      case Some(file) =>
         val writer = new PrintWriter(file)
         writer.println(jsonString)
         writer.close()
-      }
       case _ => println(jsonString)
     }
 

public/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/gearsSunburst.ssp

 #import(nl.lumc.sasc.biopet.utils.summary.Summary)
+#import(nl.lumc.sasc.biopet.utils.ConfigUtils)
 #import(java.io.File)
 <%@ var summary: Summary %>
 <%@ var sampleId: Option[String] = None %>
@@ -32,27 +33,34 @@
 
 #if (showPlot)
 <div class="row">
-        <!--
-        Javascript required for showing the sunburst plot
-        //-->
-
-        <script src="https://cdnjs.cloudflare.com/ajax/libs/d3/3.5.5/d3.min.js" charset="utf-8"></script>
-        <!-- Gears specific javascript -->
-        <script src="${rootPath}ext/js/gears.js"></script>
-
-        <h3 id='currentlevel'>Root</h3>
-        <div>
-            <span id="selection_name"></span> -
-            <span id="selection_size"></span> -
-            <span id="selection_value"></span>
-        </div>
+    <script src="https://cdnjs.cloudflare.com/ajax/libs/d3/3.5.5/d3.min.js" charset="utf-8"></script>
+    <script src="${rootPath}ext/js/gears.js"></script>
+
+    <h3 id='currentlevel'>Root</h3>
+    <div>
+        <span id="selection_name"></span> -
+        <span id="selection_size"></span> -
+        <span id="selection_value"></span>
+    </div>
+
+    <form>
+        <label><input type="radio" name="mode" value="size"> Size</label>
+        <label><input type="radio" name="mode" value="count" checked> Count</label>
+    </form>
+    <div id="sequence"></div>
 
-        <form>
-            <label><input type="radio" name="mode" value="size"> Size</label>
-            <label><input type="radio" name="mode" value="count" checked> Count</label>
-        </form>
-        <div id="sequence"></div>
+    <div id="datatable">
+    <script type="application/ecmascript">
 
-        <div id="datatable"></div>
+    #{
+        val rawreport = Map("kraken" -> summary.getValue("gears", "stats", "krakenreport"))
+        val bla = ConfigUtils.mapToJson(rawreport)
+    }#
+
+        var krakenresult = JSON.parse('<%= unescape(bla) %>');
+
+
+    </script>
+    </div>
 </div>
 #end

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

@@ -28,7 +28,6 @@ import org.broadinstitute.gatk.queue.QScript
  * Created by wyleung
  */
 class Gears(val root: Configurable) extends QScript with SummaryQScript {
-  qscript =>
   def this() = this(null)
 
   @Input(shortName = "R1", required = false)
@@ -72,7 +71,7 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript {
     val fastqFiles: List[File] = bamFile.map { bamfile =>
 
       // sambamba view -f bam -F "unmapped or mate_is_unmapped" <alnFile> > <extracted.bam>
-      val samFilterUnmapped = new SambambaView(qscript)
+      val samFilterUnmapped = new SambambaView(this)
       samFilterUnmapped.input = bamfile
       samFilterUnmapped.filter = Some("(unmapped or mate_is_unmapped) and not (secondary_alignment) and [XH] == null")
       samFilterUnmapped.output = new File(outputDir, s"$outputName.unmapped.bam")
@@ -80,7 +79,7 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript {
       add(samFilterUnmapped)
 
       // start bam to fastq (only on unaligned reads) also extract the matesam
-      val samToFastq = new SamToFastq(qscript)
+      val samToFastq = new SamToFastq(this)
       samToFastq.input = samFilterUnmapped.output
       samToFastq.stringency = Some("LENIENT")
       samToFastq.fastqR1 = new File(outputDir, s"$outputName.unmapped.R1.fq.gz")
@@ -90,7 +89,7 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript {
       add(samToFastq)
 
       // sync the fastq records
-      val fastqSync = new FastqSync(qscript)
+      val fastqSync = new FastqSync(this)
       fastqSync.refFastq = samToFastq.fastqR1
       fastqSync.inputFastq1 = samToFastq.fastqR1
       fastqSync.inputFastq2 = samToFastq.fastqR2
@@ -109,7 +108,7 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript {
     }.getOrElse(List(fastqFileR1, fastqFileR2).flatten)
 
     // start kraken
-    val krakenAnalysis = new Kraken(qscript)
+    val krakenAnalysis = new Kraken(this)
     krakenAnalysis.input = fastqFiles
     krakenAnalysis.output = new File(outputDir, s"$outputName.krkn.raw")
 
@@ -125,7 +124,7 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript {
 
     // create kraken summary file
 
-    val krakenReport = new KrakenReport(qscript)
+    val krakenReport = new KrakenReport(this)
     krakenReport.input = krakenAnalysis.output
     krakenReport.show_zeros = true
     krakenReport.output = new File(outputDir, s"$outputName.krkn.full")
@@ -134,11 +133,12 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript {
     GearsOutputFiles += ("kraken_report_input" -> krakenReport.input)
     GearsOutputFiles += ("kraken_report_output" -> krakenReport.output)
 
-    val krakenReportJSON = new KrakenReportToJson(qscript)
+    val krakenReportJSON = new KrakenReportToJson(this)
     krakenReportJSON.inputReport = krakenReport.output
     krakenReportJSON.output = new File(outputDir, s"$outputName.krkn.json")
     krakenReportJSON.skipNames = config("skipNames", default = false)
     add(krakenReportJSON)
+    addSummarizable(krakenReportJSON, "krakenreport")
 
     GearsOutputFiles += ("kraken_report_json_input" -> krakenReportJSON.inputReport)
     GearsOutputFiles += ("kraken_report_json_output" -> krakenReportJSON.output)

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

@@ -39,16 +39,13 @@ object GearsReport extends MultisampleReportBuilder {
   }
 
   def samplePage(sampleId: String, args: Map[String, Any]) = {
-    ReportPage(List(
-    ), List(
+    ReportPage(List(), List(
       "Sunburst analysis" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/gearsSunburst.ssp")
     ), args)
   }
 
   def libraryPage(sampleId: String, libId: String, args: Map[String, Any]) = {
-    ReportPage(List(
-    ), List(
-    ), args)
+    ReportPage(List(), List(), args)
   }
 
   def reportName = "Gears :: Metagenomics Report"