diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/KrakenReportToJson.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/KrakenReportToJson.scala
index 44567a15a123b84cd0f09c24a1b90d4a21d15666..8e67f29d52574f1ac444c31c6f58bc2a880d7494 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/KrakenReportToJson.scala
+++ b/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()
diff --git a/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/KrakenReportToJson.scala b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/KrakenReportToJson.scala
index 4d95619438dbc18d2597417e79d0a944fac1b02e..efc3ed383142ffc63b42960a02fe84e5ac371e1a 100644
--- a/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/KrakenReportToJson.scala
+++ b/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)
}
diff --git a/public/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/gearsSunburst.ssp b/public/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/gearsSunburst.ssp
index 8e9761cdd27d1354c45d11082aff6fc86f298efa..56aab2ebaf9f886cac261d4b181c2861e48b593a 100644
--- a/public/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/gearsSunburst.ssp
+++ b/public/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/gearsSunburst.ssp
@@ -1,4 +1,5 @@
#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
diff --git a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
index 9362fde726824639ac2c16119759498071bd1b25..ac92bf4743a4f336194a3555146597e19b234847 100644
--- a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
+++ b/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)
diff --git a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
index 02a2684c368be7cd63ddeb26f334f1a73767a86e..002dce92d237c6dacb84c83f49fb72915401b6a5 100644
--- a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
+++ b/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"