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biopet.biopet
Commit 70dd869c authored by rhpvorderman's avatar rhpvorderman
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Untangling of write summaryplotinprogress

parent ae8bf475
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Showing with 199 additions and 152 deletions
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp
View file @ 70dd869c
......@@ -20,7 +20,7 @@
<%@ var runId: Int %>
<%@ var allSamples: Seq[Sample] %>
<%@ var allLibraries: Seq[Library] %>
<%@ var alignmentSummaryPlotLines: Seq[String] %>
<%@ var alignmentSummaryPlotLines: Option[Seq[String]] %>
<%@ var alignmentSummaryResults: Map[(Int, Int), Map[String, Option[Any]]] %>
#{
val samples = sampleId match {
......@@ -48,7 +48,7 @@
</div>
#end
#if (showPlot)
#{ BammetricsReport.alignmentSummaryPlot(outputDir, "alignmentSummary", alignmentSummaryPlotLines, !sampleLevel) }#
#{ BammetricsReport.alignmentSummaryPlot(outputDir, "alignmentSummary", alignmentSummaryPlotLines.getOrElse(Seq("")), !sampleLevel) }#
<div class="panel-body">
<img src="alignmentSummary.png" class="img-responsive" />
......
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
View file @ 70dd869c
......@@ -24,6 +24,7 @@ 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
......@@ -236,12 +237,8 @@ object BammetricsReport extends ReportBuilder {
plot.title = Some("Aligned_reads")
plot.runLocal()
}
/**
* This is a generic method to create plots
* @param outputDir Outputdir of the plot
* @param prefix Files will start with this name
* @param summary Summary where the data is
* @param libraryLevel If enabled the plots will show data per library
* @param sampleId If set only this sample is shown
* @param libraryId If set onlt this library is shown
......@@ -250,29 +247,17 @@ object BammetricsReport extends ReportBuilder {
* @param xKeyList Keys to search from, first has prio over second one
* @param pipeline Query for the pipeline
* @param module Query for the module
* @param xlabel X label shown on the plot
* @param ylabel Y label shown on the plot
* @param title Title of the plot
* @param removeZero
*/
def writePlotFromSummary(outputDir: File,
prefix: String,
summary: SummaryDb,
libraryLevel: Boolean = false,
sampleId: Option[Int] = None,
libraryId: Option[Int] = None,
statsPaths: Map[String, List[String]],
yKeyList: List[String],
xKeyList: List[String],
pipeline: PipelineQuery,
module: ModuleQuery,
xlabel: Option[String] = None,
ylabel: Option[String] = None,
title: Option[String] = None,
removeZero: Boolean = true): Unit = {
val tsvFile = new File(outputDir, prefix + ".tsv")
val pngFile = new File(outputDir, prefix + ".png")
def summaryForPlot( statsPaths: Map[String, List[String]],
summary: SummaryDb,
yKeyList: List[String],
xKeyList: List[String],
pipeline: PipelineQuery,
module: ModuleQuery,
libraryLevel: Boolean = false,
sampleId: Option[Int] = None,
libraryId: Option[Int] = None
): Any = {
val results: Map[(Int, Option[Int]), Map[String, Option[Array[Any]]]] = if (libraryLevel) {
summary
.getStatsForLibraries(runId, pipeline, module, sampleId = sampleId, keyValues = statsPaths)
......@@ -282,12 +267,11 @@ object BammetricsReport extends ReportBuilder {
} else
summary
.getStatsForSamples(runId,
pipeline,
module,
sample = sampleId.map(SampleId),
keyValues = statsPaths)
pipeline,
module,
sample = sampleId.map(SampleId),
keyValues = statsPaths)
.map(x => (x._1, None) -> x._2.map(x => x._1 -> x._2.map(ConfigUtils.any2list(_).toArray)))
val tables: Array[Map[String, Array[Any]]] = results.map {
case ((sample, library), map) =>
val sampleName = Await
......@@ -304,6 +288,33 @@ object BammetricsReport extends ReportBuilder {
.getOrElse(Array())
)
}.toArray
tables
}
/**
* This is a generic method to create plots
* @param outputDir Outputdir of the plot
* @param prefix Files will start with this name
* @param tables Tables to be written
* @param yKeyList Keys to search from, first has prio over second one
* @param xKeyList Keys to search from, first has prio over second one
* @param xlabel X label shown on the plot
* @param ylabel Y label shown on the plot
* @param title Title of the plot
* @param removeZero
*/
def writePlotFromSummary(outputDir: File,
prefix: String,
tables: Array[Map[String, Array[Any]]],
xKeyList: List[String],
yKeyList: List[String],
xlabel: Option[String] = None,
ylabel: Option[String] = None,
title: Option[String] = None,
removeZero: Boolean = true): Unit = {
val tsvFile = new File(outputDir, prefix + ".tsv")
val pngFile = new File(outputDir, prefix + ".png")
writeTableToTsv(tsvFile, mergeTables(tables, yKeyList.head), yKeyList.head)
......@@ -312,7 +323,7 @@ object BammetricsReport extends ReportBuilder {
xlabel = xlabel,
ylabel = ylabel,
title = title,
hideLegend = results.size > 40,
hideLegend = tables.size > 40, /* changed from results.size. Original results in summaryForPlot*/
removeZero = removeZero).runLocal()
}
......@@ -327,7 +338,7 @@ object BammetricsReport extends ReportBuilder {
*/
def insertSizePlot(outputDir: File,
prefix: String,
summary: SummaryDb,
tables: Array[Map[String, Array[Any]]],
libraryLevel: Boolean = false,
sampleId: Option[Int] = None,
libraryId: Option[Int] = None): Unit = {
......@@ -339,7 +350,7 @@ object BammetricsReport extends ReportBuilder {
writePlotFromSummary(
outputDir,
prefix,
summary,
tables,
libraryLevel,
sampleId,
libraryId,
......@@ -364,7 +375,12 @@ object BammetricsReport extends ReportBuilder {
"mapping_quality" -> List("mapping_quality", "histogram", "values"),
"count" -> List("mapping_quality", "histogram", "counts")
)
summaryForPlot(statsPaths,
"mapping_quality" :: Nil,
"count" :: Nil,
"bammetrics",
"bamstats"
)
writePlotFromSummary(
outputDir,
prefix,
......@@ -373,10 +389,8 @@ object BammetricsReport extends ReportBuilder {
sampleId,
libraryId,
statsPaths,
"mapping_quality" :: Nil,
"count" :: Nil,
"bammetrics",
"bamstats",
,
"Mapping quality",
"Reads",
"Mapping quality"
......@@ -385,7 +399,7 @@ object BammetricsReport extends ReportBuilder {
def clippingPlot(outputDir: File,
prefix: String,
summary: SummaryDb,
tables: Array[Map[String, Array[Any]]],
libraryLevel: Boolean = false,
sampleId: Option[Int] = None,
libraryId: Option[Int] = None): Unit = {
......@@ -423,7 +437,7 @@ object BammetricsReport extends ReportBuilder {
*/
def wgsHistogramPlot(outputDir: File,
prefix: String,
summary: SummaryDb,
tables: Array[Map[String, Array[Any]]],
libraryLevel: Boolean = false,
sampleId: Option[Int] = None,
libraryId: Option[Int] = None): Unit = {
......@@ -462,7 +476,7 @@ object BammetricsReport extends ReportBuilder {
*/
def rnaHistogramPlot(outputDir: File,
prefix: String,
summary: SummaryDb,
tables: Array[Map[String, Array[Any]]],
libraryLevel: Boolean = false,
sampleId: Option[Int] = None,
libraryId: Option[Int] = None): Unit = {
......@@ -513,14 +527,17 @@ object BammetricsReport extends ReportBuilder {
}
}
object BamMetricsAlignmentSummary {
object BamMetricsAlignmentReport {
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] = {
libId: Option[Int] = None,
sampleLevel: Boolean = false,
showPlot: Boolean = false,
showIntro: Boolean = true,
showTable: Boolean = true): Map[String,Any] = {
val statsPaths = Map(
"All" -> List("flagstats", "All"),
......@@ -529,10 +546,38 @@ object BamMetricsAlignmentSummary {
"NotPrimaryAlignment" -> List("flagstats", "NotPrimaryAlignment")
)
val alignmentSummaryResults = summary.getStatsForLibraries(runId,"bammetrics","bamstats", sampleId, statsPaths)
val alignmentSummaryPlotLines = BammetricsReport.alignmentSummaryPlotLines(summary,sampleId,!sampleLevel)
val alignmentSummaryPlotLines: Option[Seq[String]] =
if (showPlot)
Some(BammetricsReport.alignmentSummaryPlotLines(summary,sampleId,!sampleLevel))
else None
Map(
"alignmentSummaryResults" -> alignmentSummaryResults,
"alignmentSummaryPlotLines" -> alignmentSummaryPlotLines
"alignmentSummaryPlotLines" -> alignmentSummaryPlotLines,
"sampleLevel" -> sampleLevel,
"showPlot" -> showPlot,
"showIntro" -> showIntro,
"showTable" -> showTable,
"sampleId" -> sampleId,
"libId" -> libId
)
}
}
object BamMetricsMappingQuality {
def values(summary: SummaryDb,
runId: Int,
allSamples: Seq[Sample],
allLibraries: Seq[Library],
sampleId: Option[Int],
libId: Option[Int],
sampleLevel: Boolean= false,
showPlot: Boolean = false,
showIntro: Boolean = true,
showTable: Boolean = true): Map[String,Any] = {
val samples = sampleId match {
case Some(id) => allSamples.filter(_.id == id).toList
case _ => allSamples.toList
}
val
}
}
\ No newline at end of file
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala
View file @ 70dd869c
......@@ -14,14 +14,10 @@
*/
package nl.lumc.sasc.biopet.pipelines.mapping
import nl.lumc.sasc.biopet.core.report.{
MultisampleReportBuilder,
ReportBuilderExtension,
ReportPage,
ReportSection
}
import nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport
import nl.lumc.sasc.biopet.core.report.{MultisampleReportBuilder, ReportBuilderExtension, ReportPage, ReportSection}
import nl.lumc.sasc.biopet.pipelines.bammetrics.{BamMetricsAlignmentReport, BammetricsReport}
import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
import nl.lumc.sasc.biopet.pipelines.gears.GearsKronaPlot
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._
import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._
......@@ -61,20 +57,20 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
.map(x => ExtFile("/nl/lumc/sasc/biopet/pipelines/gears/report/ext/" + x, x))
/** Root page for the carp report */
def indexPage: Future[ReportPage] = Future {
def indexPage: Future[ReportPage] = {
val krakenExecuted = Await.result(summary.getStatsSize(runId,
"gearskraken",
"krakenreport",
library = NoLibrary,
mustHaveSample = true),
Duration.Inf) >= 1
"gearskraken",
"krakenreport",
library = NoLibrary,
mustHaveSample = true),
Duration.Inf) >= 1
val centrifugeExecuted = Await.result(summary.getStatsSize(runId,
"gearscentrifuge",
"centrifuge_report",
library = NoLibrary,
mustHaveSample = true),
Duration.Inf) >= 1
"gearscentrifuge",
"centrifuge_report",
library = NoLibrary,
mustHaveSample = true),
Duration.Inf) >= 1
val wgsExecuted = Await.result(
summary.getStatsSize(runId, "bammetrics", "wgs", library = NoLibrary, mustHaveSample = true),
Duration.Inf) >= 1
......@@ -83,100 +79,106 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
Duration.Inf) >= 1
val insertsizeExecuted = summary
.getStatsForSamples(runId,
"bammetrics",
"CollectInsertSizeMetrics",
keyValues = Map("metrics" -> List("metrics")))
"bammetrics",
"CollectInsertSizeMetrics",
keyValues = Map("metrics" -> List("metrics")))
.exists(_._2("metrics").isDefined)
val mappingExecuted = Await.result(
summary.getStatsSize(runId, "mapping", NoModule, mustHaveLibrary = true),
Duration.Inf) >= 1
val mappingSettings = summary.getSettingsForLibraries(runId,
"mapping",
NoModule,
keyValues =
Map("paired" -> List("paired")))
"mapping",
NoModule,
keyValues =
Map("paired" -> List("paired")))
val pairedFound = !mappingExecuted || mappingSettings.exists(_._2.exists(_._2 == Option(true)))
val flexiprepExecuted = Await
.result(summary.getStatsSize(runId, "flexiprep", mustHaveLibrary = true), Duration.Inf) >= 1
ReportPage(
List("Samples" -> generateSamplesPage(pageArgs)) ++
(if (krakenExecuted)
List(
"Dustbin analysis - Kraken" -> Future.successful(
ReportPage(List(),
List("Krona plot" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp")),
Map())))
else Nil) ++ (if (centrifugeExecuted)
List(
"Centrifuge analysis" -> Future.successful(ReportPage(
List("Non-unique" -> Future.successful(
ReportPage(List(),
List("All mappings" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
Map("summaryStatsTag" -> "centrifuge_report"))),
Map()))),
List("Unique mappings" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
Map("summaryStatsTag" -> "centrifuge_unique_report"))),
Map("summaryModuleTag" -> "gearscentrifuge",
"centrifugeTag" -> Some("centrifuge"))
)))
else Nil) ++
List(
"Reference" -> Future.successful(
ReportPage(
List(),
List(
"Reference" -> ReportSection("/nl/lumc/sasc/biopet/core/report/reference.ssp",
Map("pipeline" -> pipelineName))
),
Map()))),
List("Report" -> frontSection) ++
additionalSections ++
List(
"Alignment" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp",
Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)),
"Mapping Quality" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/mappingQuality.ssp",
Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)),
"Clipping" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/clipping.ssp",
Map("sampleLevel" -> true,
"showPlot" -> true,
"showTable" -> false))
) ++
(if (pairedFound && insertsizeExecuted)
List(
"Insert Size" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp",
Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)))
else Nil) ++
(if (wgsExecuted)
List(
"Whole genome coverage" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp",
Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)))
else Nil) ++
(if (rnaExecuted)
List(
"Rna coverage" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/rnaHistogram.ssp",
Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)))
else Nil) ++
(if (flexiprepExecuted)
List(
"QC reads" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp",
Map("showPlot" -> true, "showTable" -> false)),
"QC bases" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp",
Map("showPlot" -> true, "showTable" -> false))
)
else Nil),
pageArgs ++ Map("pipeline" -> pipelineName)
)
val krakenDustbinAnalysis = GearsKronaPlot.values(summary, runId, "gearskraken", "krakenreport", samples, libraries, sampleId, libId )
val centrifugeAnalysis = GearsKronaPlot.values(summary, runId, "gearscentrifuge", "centrifuge_report", samples, libraries, sampleId, libId )
val centrifugeUniqueAnalysis = GearsKronaPlot.values(summary, runId, "gearscentrifuge", "centrifuge_unique_report", samples, libraries, sampleId, libId )
val alignmentSummary = BamMetricsAlignmentReport.values(summary, runId, samples, libraries, sampleId, libId, sampleLevel =true,showPlot=true,showTable=false)
Future {
ReportPage(
List("Samples" -> generateSamplesPage(pageArgs)) ++
(if (krakenExecuted)
List(
"Dustbin analysis - Kraken" -> Future.successful(
ReportPage(List(),
List("Krona plot" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",krakenDustbinAnalysis)),
Map())))
else Nil) ++ (if (centrifugeExecuted)
List(
"Centrifuge analysis" -> Future.successful(ReportPage(
List("Non-unique" -> Future.successful(
ReportPage(List(),
List("All mappings" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
centrifugeAnalysis)),
Map()))),
List("Unique mappings" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
centrifugeUniqueAnalysis)),
Map("summaryModuleTag" -> "gearscentrifuge",
"centrifugeTag" -> Some("centrifuge"))
)))
else Nil) ++
List(
"Reference" -> Future.successful(
ReportPage(
List(),
List(
"Reference" -> ReportSection("/nl/lumc/sasc/biopet/core/report/reference.ssp",
Map("pipeline" -> pipelineName))
),
Map()))),
List("Report" -> frontSection) ++
additionalSections ++
List(
"Alignment" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp",
alignmentSummary),
"Mapping Quality" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/mappingQuality.ssp",
Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)),
"Clipping" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/clipping.ssp",
Map("sampleLevel" -> true,
"showPlot" -> true,
"showTable" -> false))
) ++
(if (pairedFound && insertsizeExecuted)
List(
"Insert Size" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp",
Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)))
else Nil) ++
(if (wgsExecuted)
List(
"Whole genome coverage" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp",
Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)))
else Nil) ++
(if (rnaExecuted)
List(
"Rna coverage" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/rnaHistogram.ssp",
Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)))
else Nil) ++
(if (flexiprepExecuted)
List(
"QC reads" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp",
Map("showPlot" -> true, "showTable" -> false)),
"QC bases" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp",
Map("showPlot" -> true, "showTable" -> false))
)
else Nil),
pageArgs ++ Map("pipeline" -> pipelineName)
)
}
}
/** Single sample page */
......
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