From f4614adfdcdd3c0c7446994308710ffecf9d41b4 Mon Sep 17 00:00:00 2001 From: rhpvorderman Date: Mon, 31 Jul 2017 11:56:43 +0200 Subject: [PATCH] Defutured alignmentSummary.ssp --- .../pipelines/bammetrics/alignmentSummary.ssp | 16 +-- .../bammetrics/BammetricsReport.scala | 99 +++++++++++++------ 2 files changed, 76 insertions(+), 39 deletions(-) diff --git a/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp b/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp index 347e9ac9b..89a7d51a0 100644 --- a/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp +++ b/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp @@ -1,4 +1,5 @@ -#import(nl.lumc.sasc.biopet.utils.summary.db.Schema._) +#import(nl.lumc.sasc.biopet.utils.summary.db.Schema.Sample) +#import(nl.lumc.sasc.biopet.utils.summary.db.Schema.Library) #import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb) #import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._) #import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._) @@ -19,6 +20,8 @@ <%@ var runId: Int %> <%@ var allSamples: Seq[Sample] %> <%@ var allLibraries: Seq[Library] %> +<%@ var alignmentSummaryPlotLines: Seq[String] %> +<%@ var alignmentSummaryResults: Map[(Int, Int), Map[String, Option[Any]]] %> #{ val samples = sampleId match { case Some(id) => allSamples.filter(_.id == id).toList @@ -45,7 +48,7 @@ #end #if (showPlot) -#{ BammetricsReport.alignmentSummaryPlot(outputDir, "alignmentSummary", summary, !sampleLevel, sampleId = sampleId) }# +#{ BammetricsReport.alignmentSummaryPlot(outputDir, "alignmentSummary", alignmentSummaryPlotLines, !sampleLevel) }#
@@ -95,11 +98,10 @@ "Duplicates" -> List("flagstats", "Duplicates"), "NotPrimaryAlignment" -> List("flagstats", "NotPrimaryAlignment") ) - val results = summary.getStatKeys(runId, "bammetrics", "bamstats", sample = sample.id, library = libId.map(LibraryId).getOrElse(NoLibrary), keyValues = statsPaths) - val total = results("All").getOrElse(0L).asInstanceOf[Long] - val mapped = results("Mapped").getOrElse(0L).asInstanceOf[Long] - val duplicates = results("Duplicates").getOrElse(0L).asInstanceOf[Long] - val secondary = results("NotPrimaryAlignment").getOrElse(0L).asInstanceOf[Long] + val total = alignmentSummaryResults(sample.id,libId)("All").getOrElse(0L).asInstanceOf[Long] + val mapped = alignmentSummaryResults(sample.id, libId)("Mapped").getOrElse(0L).asInstanceOf[Long] + val duplicates = alignmentSummaryResults(sample.id,libId)("Duplicates").getOrElse(0L).asInstanceOf[Long] + val secondary = alignmentSummaryResults(sample.id,libId)("NotPrimaryAlignment").getOrElse(0L).asInstanceOf[Long] }# ${total} ${mapped} diff --git a/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala b/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala index 8141d162c..1363efaa3 100644 --- a/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala +++ b/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala @@ -17,18 +17,14 @@ package nl.lumc.sasc.biopet.pipelines.bammetrics import java.io.{File, PrintWriter} import nl.lumc.sasc.biopet.utils.config.Configurable -import nl.lumc.sasc.biopet.core.report.{ - ReportBuilder, - ReportBuilderExtension, - ReportPage, - ReportSection -} +import nl.lumc.sasc.biopet.core.report.{ReportBuilder, ReportBuilderExtension, ReportPage, ReportSection} import nl.lumc.sasc.biopet.utils.ConfigUtils import nl.lumc.sasc.biopet.utils.rscript.{LinePlot, StackedBarPlot} import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._ import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._ - +import nl.lumc.sasc.biopet.utils.summary.db.Schema._ +import scala.collection.mutable.ArrayBuffer import scala.concurrent.{Await, Future} import scala.concurrent.duration.Duration @@ -154,25 +150,15 @@ object BammetricsReport extends ReportBuilder { } /** - * Generate a stackbar plot for alignment stats + * Generates the lines for alignmentSummaryPlot * - * @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 + * * @param libraryLevel Default false, when set true plot will be based on library stats instead of sample stats */ - def alignmentSummaryPlot(outputDir: File, - prefix: String, - summary: SummaryDb, - libraryLevel: Boolean = false, - sampleId: Option[Int] = None): Unit = { - 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("\tMapped\tDuplicates\tUnmapped\tSecondary") - + def alignmentSummaryPlotLines(summary: SummaryDb, + sampleId: Option[Int] = None, + libraryLevel: Boolean = false): Seq[String] = { val statsPaths = Map( "Mapped" -> List("flagstats", "Mapped"), "Duplicates" -> List("flagstats", "Duplicates"), @@ -183,19 +169,20 @@ object BammetricsReport extends ReportBuilder { val results: Map[(Int, Option[Int]), Map[String, Option[Any]]] = if (libraryLevel) { summary .getStatsForLibraries(runId, - "bammetrics", - "bamstats", - sampleId = sampleId, - keyValues = statsPaths) + "bammetrics", + "bamstats", + sampleId = sampleId, + keyValues = statsPaths) .map(x => (x._1._1, Some(x._1._2)) -> x._2) } else summary .getStatsForSamples(runId, - "bammetrics", - "bamstats", - sample = sampleId.map(SampleId), - keyValues = statsPaths) + "bammetrics", + "bamstats", + sample = sampleId.map(SampleId), + keyValues = statsPaths) .map(x => (x._1, None) -> x._2) + val summaryPlotLines = ArrayBuffer[String]() for (((s, l), result) <- results) { val sampleName: String = summary.getSampleName(s).map(_.get) @@ -212,16 +199,40 @@ object BammetricsReport extends ReportBuilder { sb.append(duplicates + "\t") sb.append((total - mapped) + "\t") sb.append(secondary) - tsvWriter.println(sb.toString) + summaryPlotLines += sb.toString } + summaryPlotLines + } + + /** + * Generate a stackbar plot for alignment stats + * + * @param outputDir OutputDir for the tsv and png file + * @param prefix Prefix of the tsv and png file + * @param summaryPlotLines A sequence of strings written to the summary tsv + * @param libraryLevel Default false, when set true plot will be based on library stats instead of sample stats + */ + def alignmentSummaryPlot(outputDir: File, + prefix: String, + summaryPlotLines: Seq[String], + libraryLevel: Boolean = false + ): Unit = { + 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("\tMapped\tDuplicates\tUnmapped\tSecondary") + for (line <- summaryPlotLines) { + tsvWriter.println(line) + } tsvWriter.close() val plot = new StackedBarPlot(null) plot.input = tsvFile plot.output = pngFile plot.ylabel = Some("Reads") - plot.width = Some(200 + (results.size * 10)) + plot.width = Some(200 + (summaryPlotLines.size * 10)) plot.title = Some("Aligned_reads") plot.runLocal() } @@ -501,3 +512,27 @@ object BammetricsReport extends ReportBuilder { writer.close() } } + +object BamMetricsAlignmentSummary { + def values(summary: SummaryDb, + runId: Int, + allSamples: Seq[Sample], + allLibraries: Seq[Library], + sampleId: Option[Int] = None, + libId: Option[Int], + sampleLevel: Boolean = false): Map[String,Any] = { + + val statsPaths = Map( + "All" -> List("flagstats", "All"), + "Mapped" -> List("flagstats", "Mapped"), + "Duplicates" -> List("flagstats", "Duplicates"), + "NotPrimaryAlignment" -> List("flagstats", "NotPrimaryAlignment") + ) + val alignmentSummaryResults = summary.getStatsForLibraries(runId,"bammetrics","bamstats", sampleId, statsPaths) + val alignmentSummaryPlotLines = BammetricsReport.alignmentSummaryPlotLines(summary,sampleId,!sampleLevel) + Map( + "alignmentSummaryResults" -> alignmentSummaryResults, + "alignmentSummaryPlotLines" -> alignmentSummaryPlotLines + ) + } +} -- GitLab