ShivaReport.scala 7.62 KB
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/**
 * Biopet is built on top of GATK Queue for building bioinformatic
 * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
 * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
 * should also be able to execute Biopet tools and pipelines.
 *
 * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
 *
 * Contact us at: sasc@lumc.nl
 *
 * A dual licensing mode is applied. The source code within this project that are
 * not part of GATK Queue is freely available for non-commercial use under an AGPL
 * license; For commercial users or users who do not want to follow the AGPL
 * license, please contact us to obtain a separate license.
 */
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package nl.lumc.sasc.biopet.pipelines.shiva

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import java.io.{ File, PrintWriter }
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import nl.lumc.sasc.biopet.pipelines.mapping.MultisampleMappingReportTrait
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import nl.lumc.sasc.biopet.utils.config.Configurable
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import nl.lumc.sasc.biopet.core.report._
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import nl.lumc.sasc.biopet.utils.summary.{ Summary, SummaryValue }
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import nl.lumc.sasc.biopet.utils.rscript.StackedBarPlot
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import nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport
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import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport

/**
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 * With this extension the report is executed within a pipeline
 *
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 * Created by pjvan_thof on 3/30/15.
 */
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class ShivaReport(val root: Configurable) extends ReportBuilderExtension {
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  def builder = ShivaReport
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}

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/** Object for report generation for Shiva pipeline */
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object ShivaReport extends MultisampleMappingReportTrait {
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  def variantcallingExecuted = summary.getValue("shiva", "settings", "multisample_variantcalling") match {
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    case Some(true) => true
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    case _          => false
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  }

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  override def frontSection = ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/shivaFront.ssp")

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  override def extFiles = super.extFiles ++ List("js/gears.js")
    .map(x => ExtFile("/nl/lumc/sasc/biopet/pipelines/gears/report/ext/" + x, x))

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  /** Root page for the shiva report */
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  override def indexPage = {
    val variantcallingSection = (if (variantcallingExecuted) List("Variantcalling" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp",
      Map("showPlot" -> true, "showTable" -> false)))
    else Nil)

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    val regions = regionsPage
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    val oldPage = super.indexPage

    oldPage.copy(sections = variantcallingSection ++ oldPage.sections, subPages = oldPage.subPages ++ regionsPage)
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  }
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  /** Generate a page with all target coverage stats */
  def regionsPage: Option[(String, ReportPage)] = {
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    val roi = summary.getValue("shiva", "settings", "regions_of_interest")
    val amplicon = summary.getValue("shiva", "settings", "amplicon_bed")

    var regionPages: Map[String, ReportPage] = Map()

    def createPage(name: String, amplicon: Boolean = false): ReportPage = {
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      ReportPage(
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        List(),
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        List("Coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsMultiTable.ssp")),
        Map("target" -> name)
      )
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    }

    amplicon match {
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      case Some(x: String) => regionPages += (x + " (Amplicon)") -> createPage(x, amplicon = true)
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      case _               =>
    }

    roi match {
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      case Some(x: String)  => regionPages += x -> createPage(x, amplicon = false)
      case Some(x: List[_]) => x.foreach(x => regionPages += x.toString -> createPage(x.toString, amplicon = false))
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      case _                =>
    }

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    if (regionPages.nonEmpty) Some("Regions" -> ReportPage(
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      regionPages.map(p => p._1 -> ReportPage(Nil,
        List(
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          "Variants" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp", Map("showPlot" -> true)),
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          "Coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsMultiTable.ssp")
        ),
        Map("target" -> Some(p._1.stripSuffix(" (Amplicon)")))
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      )).toList.sortBy(_._1),
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      List(),
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      Map())
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    )
    else None
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  }

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  /** Files page, can be used general or at sample level */
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  override def filesPage: ReportPage = {
    val vcfFilesSection = if (variantcallingExecuted) List("VCF files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/outputVcfFiles.ssp",
      Map("sampleId" -> None))) else Nil
    val oldPage = super.filesPage
    oldPage.copy(sections = oldPage.sections ++ vcfFilesSection)
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  }

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  /** Single sample page */
  override def samplePage(sampleId: String, args: Map[String, Any]): ReportPage = {
    val variantcallingSection = if (variantcallingExecuted) List("Variantcalling" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp")) else Nil
    val oldPage = super.samplePage(sampleId, args)
    oldPage.copy(sections = variantcallingSection ++ oldPage.sections)
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  }

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  /** Name of the report */
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  def reportName = "Shiva Report"
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  /**
   * Generate a stackbar plot for found variants
   * @param outputDir OutputDir for the tsv and png file
   * @param prefix Prefix of the tsv and png file
   * @param summary Summary class
   * @param libraryLevel Default false, when set true plot will be based on library stats instead of sample stats
   * @param sampleId Default it selects all sampples, when sample is giving it limits to selected sample
   */
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  def variantSummaryPlot(outputDir: File,
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                         prefix: String,
                         summary: Summary,
                         libraryLevel: Boolean = false,
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                         sampleId: Option[String] = None,
                         caller: String = "final",
                         target: Option[String] = None): Unit = {
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    val tsvFile = new File(outputDir, prefix + ".tsv")
    val pngFile = new File(outputDir, prefix + ".png")
    val tsvWriter = new PrintWriter(tsvFile)
    if (libraryLevel) tsvWriter.print("Library") else tsvWriter.print("Sample")
    tsvWriter.println("\tHomVar\tHet\tHomRef\tNoCall")

    def getLine(summary: Summary, sample: String, lib: Option[String] = None): String = {
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      val path = target match {
        case Some(t) => List("shivavariantcalling", "stats", s"multisample-vcfstats-$caller-$t", "genotype")
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        case _       => List("shivavariantcalling", "stats", s"multisample-vcfstats-$caller", "genotype")
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      }
      val homVar = new SummaryValue(path :+ "HomVar", summary, Some(sample), lib).value.getOrElse(0).toString.toLong
      val homRef = new SummaryValue(path :+ "HomRef", summary, Some(sample), lib).value.getOrElse(0).toString.toLong
      val noCall = new SummaryValue(path :+ "NoCall", summary, Some(sample), lib).value.getOrElse(0).toString.toLong
      val het = new SummaryValue(path :+ "Het", summary, Some(sample), lib).value.getOrElse(0).toString.toLong
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      val sb = new StringBuffer()
      if (lib.isDefined) sb.append(sample + "-" + lib.get + "\t") else sb.append(sample + "\t")
      sb.append(homVar + "\t")
      sb.append(het + "\t")
      sb.append(homRef + "\t")
      sb.append(noCall)
      sb.toString
    }

    if (libraryLevel) {
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      for (
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        sample <- summary.samples if sampleId.isEmpty || sample == sampleId.get;
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        lib <- summary.libraries(sample)
      ) {
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        tsvWriter.println(getLine(summary, sample, Some(lib)))
      }
    } else {
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      for (sample <- summary.samples if sampleId.isEmpty || sample == sampleId.get) {
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        tsvWriter.println(getLine(summary, sample))
      }
    }

    tsvWriter.close()

    val plot = new StackedBarPlot(null)
    plot.input = tsvFile
    plot.output = pngFile
    plot.ylabel = Some("VCF records")
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    if (libraryLevel) {
      plot.width = Some(200 + (summary.libraries.filter(s => sampleId.getOrElse(s._1) == s._1).foldLeft(0)(_ + _._2.size) * 10))
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    } else plot.width = Some(200 + (summary.samples.count(s => sampleId.getOrElse(s) == s) * 10))
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    plot.runLocal()
  }
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}