ShivaReport.scala 7.49 KB
Newer Older
Peter van 't Hof's avatar
Peter van 't Hof committed
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
/**
 * 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.
 */
16
17
package nl.lumc.sasc.biopet.pipelines.shiva

18
import java.io.{File, PrintWriter}
19

20
import nl.lumc.sasc.biopet.core.report._
21
import nl.lumc.sasc.biopet.pipelines.mapping.MultisampleMappingReportTrait
Peter van 't Hof's avatar
Peter van 't Hof committed
22
import nl.lumc.sasc.biopet.utils.config.Configurable
23
import nl.lumc.sasc.biopet.utils.rscript.StackedBarPlot
24
import nl.lumc.sasc.biopet.utils.summary.{Summary, SummaryValue}
25
26

/**
27
28
 * With this extension the report is executed within a pipeline
 *
29
30
 * Created by pjvan_thof on 3/30/15.
 */
31
class ShivaReport(val root: Configurable) extends ReportBuilderExtension {
32
  def builder = ShivaReport
33
34
}

35
/** Object for report generation for Shiva pipeline */
36
object ShivaReport extends MultisampleMappingReportTrait {
37

38
  def variantcallingExecuted = summary.getValue("shiva", "settings", "multisample_variantcalling") match {
Peter van 't Hof's avatar
Peter van 't Hof committed
39
    case Some(true) => true
Peter van 't Hof's avatar
Peter van 't Hof committed
40
    case _          => false
41
42
  }

43
44
  override def frontSection = ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/shivaFront.ssp")

45
46
47
  override def extFiles = super.extFiles ++ List("js/gears.js")
    .map(x => ExtFile("/nl/lumc/sasc/biopet/pipelines/gears/report/ext/" + x, x))

48
  /** Root page for the shiva report */
49
50
51
52
53
  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)

54
    val regions = regionsPage
55
56
57
    val oldPage = super.indexPage

    oldPage.copy(sections = variantcallingSection ++ oldPage.sections, subPages = oldPage.subPages ++ regionsPage)
58
  }
59

60
61
  /** Generate a page with all target coverage stats */
  def regionsPage: Option[(String, ReportPage)] = {
62
63
64
65
66
67
    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 = {
Peter van 't Hof's avatar
Peter van 't Hof committed
68
      ReportPage(
69
        List(),
Peter van 't Hof's avatar
Peter van 't Hof committed
70
71
72
        List("Coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsMultiTable.ssp")),
        Map("target" -> name)
      )
73
74
75
    }

    amplicon match {
76
      case Some(x: String) => regionPages += (x + " (Amplicon)") -> createPage(x, amplicon = true)
77
78
79
80
      case _               =>
    }

    roi match {
81
82
      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))
83
84
85
      case _                =>
    }

Peter van 't Hof's avatar
Peter van 't Hof committed
86
    if (regionPages.nonEmpty) Some("Regions" -> ReportPage(
87
88
      regionPages.map(p => p._1 -> ReportPage(Nil,
        List(
Peter van 't Hof's avatar
Peter van 't Hof committed
89
          "Variants" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp", Map("showPlot" -> true)),
90
91
92
          "Coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsMultiTable.ssp")
        ),
        Map("target" -> Some(p._1.stripSuffix(" (Amplicon)")))
93
      )).toList.sortBy(_._1),
94
      List(),
Peter van 't Hof's avatar
Peter van 't Hof committed
95
      Map())
Peter van 't Hof's avatar
Peter van 't Hof committed
96
97
    )
    else None
98
99
  }

100
  /** Files page, can be used general or at sample level */
101
102
103
104
105
  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)
106
107
  }

108
109
110
111
112
  /** 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)
113
114
  }

115
  /** Name of the report */
116
  def reportName = "Shiva Report"
117

118
119
120
121
122
123
124
125
  /**
   * 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
   */
126
  def variantSummaryPlot(outputDir: File,
127
128
129
                         prefix: String,
                         summary: Summary,
                         libraryLevel: Boolean = false,
130
131
132
                         sampleId: Option[String] = None,
                         caller: String = "final",
                         target: Option[String] = None): Unit = {
133
134
135
136
137
138
139
    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 = {
140
141
      val path = target match {
        case Some(t) => List("shivavariantcalling", "stats", s"multisample-vcfstats-$caller-$t", "genotype")
Peter van 't Hof's avatar
Peter van 't Hof committed
142
        case _       => List("shivavariantcalling", "stats", s"multisample-vcfstats-$caller", "genotype")
143
144
145
146
147
      }
      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
148
149
150
151
152
153
154
155
156
157
      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) {
158
      for (
159
        sample <- summary.samples if sampleId.isEmpty || sample == sampleId.get;
160
161
        lib <- summary.libraries(sample)
      ) {
162
163
164
        tsvWriter.println(getLine(summary, sample, Some(lib)))
      }
    } else {
165
      for (sample <- summary.samples if sampleId.isEmpty || sample == sampleId.get) {
166
167
168
169
170
171
172
173
174
175
        tsvWriter.println(getLine(summary, sample))
      }
    }

    tsvWriter.close()

    val plot = new StackedBarPlot(null)
    plot.input = tsvFile
    plot.output = pngFile
    plot.ylabel = Some("VCF records")
176
177
    if (libraryLevel) {
      plot.width = Some(200 + (summary.libraries.filter(s => sampleId.getOrElse(s._1) == s._1).foldLeft(0)(_ + _._2.size) * 10))
178
    } else plot.width = Some(200 + (summary.samples.count(s => sampleId.getOrElse(s) == s) * 10))
179
180
    plot.runLocal()
  }
181
}