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biopet.biopet
Commit e5b7192d authored by Vorderman's avatar Vorderman
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Defutured covstats.ssp

parent e2e3d2a5
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Showing with 485 additions and 318 deletions
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsPlot.ssp
View file @ e5b7192d
......@@ -7,6 +7,7 @@
#import(scala.concurrent.Await)
#import(scala.concurrent.duration.Duration)
#import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
#import(nl.lumc.sasc.biopet.utils.summary.db.Schema)
#import(java.io.File)
<%@ var summary: SummaryDb %>
<%@ var sampleId: Option[Int] %>
......@@ -16,16 +17,14 @@
<%@ var target: Option[String] %>
<%@ var runId: Int %>
<%@ var fields: List[String] = List("mean", "median", "max", "horizontal", "frac_min_10x", "frac_min_20x", "frac_min_30x", "frac_min_40x", "frac_min_50x") %>
<%@ var plotFile: Option[Schema.File] %>
<%@ var values: Map[String, Option[Any]] %>
#{
val moduleName = target.get + "_cov_stats"
val statsPaths = fields.map(x => x -> List("coverage", "_all", x)).toMap
val plotFile = Await.result(summary.getFile(runId, PipelineName(metricsTag), ModuleName(moduleName), sampleId.map(SampleId).get, libId.map(LibraryId).getOrElse(NoLibrary), "plot"), Duration.Inf)
val originalPlot = new File(plotFile.get.path)
val plot = new File(outputDir, target.get + "_cov_stats.png")
val values = summary.getStatKeys(runId, PipelineName(metricsTag), ModuleName(moduleName), sampleId.map(SampleId).get, libId.map(LibraryId).getOrElse(NoLibrary), statsPaths)
if (originalPlot.exists()) IoUtils.copyFile(originalPlot, plot)
}#
<img src="${plot.getName}">
......
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp
View file @ e5b7192d
......@@ -85,6 +85,7 @@
#for (field <- fields)
<td>${results(field)}</td>
#end
#end
</tr>
#end
#end
......
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
View file @ e5b7192d
......@@ -23,13 +23,11 @@ import nl.lumc.sasc.biopet.core.report.{
ReportPage,
ReportSection
}
import nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport.mappingQualityPlotTables
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}
......@@ -71,11 +69,20 @@ object BammetricsReport extends ReportBuilder {
)
}
/** Generates values for bamMetricsPage */
def bamMetricsPageValues(summary: SummaryDb,
sampleId: Option[Int],
libId: Option[Int],
metricsTag: String = "bammetrics"): Map[String, Any] = {
Map("" -> "")
}
/** Generates a page with alignment stats */
def bamMetricsPage(summary: SummaryDb,
sampleId: Option[Int],
libId: Option[Int],
metricsTag: String = "bammetrics"): Future[ReportPage] = Future {
metricsTag: String = "bammetrics"): Future[ReportPage] = {
val wgsExecuted = summary.getStatsSize(runId,
metricsTag,
"wgs",
......@@ -115,6 +122,15 @@ object BammetricsReport extends ReportBuilder {
case _ => Nil
}
val covstatsPlotValuesArray = ArrayBuffer[(String, Map[String,Any])]()
for (t <- targets) {
covstatsPlotValuesArray += Tuple2(t,BammetricsReportPage.covstatsPlotValues(summary, runId, sampleId, libId, Some(t)))
}
val covstatsPlotValuesList = covstatsPlotValuesArray.toList
Future {
ReportPage(
if (targets.isEmpty) List()
else
......@@ -122,9 +138,9 @@ object BammetricsReport extends ReportBuilder {
"Targets" -> Future.successful(
ReportPage(
List(),
targets.map(t =>
t -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsPlot.ssp",
Map("target" -> Some(t)))),
covstatsPlotValuesList.map(covstats =>
covstats._1 -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsPlot.ssp",
covstats._2)),
Map()))),
List(
"Summary" -> ReportSection(
......@@ -155,6 +171,7 @@ object BammetricsReport extends ReportBuilder {
Map("metricsTag" -> metricsTag)
)
}
}
/**
* Generates the lines for alignmentSummaryPlot
......
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReportPage.scala
View file @ e5b7192d
......@@ -2,10 +2,14 @@ package nl.lumc.sasc.biopet.pipelines.bammetrics
import nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport.mappingQualityPlotTables
import nl.lumc.sasc.biopet.utils.summary.db.Schema.{Library, Sample}
import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb
import nl.lumc.sasc.biopet.utils.summary.db.{Schema, SummaryDb}
import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._
import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._
import scala.concurrent.Await
import scala.concurrent.duration.Duration
import java.io.File
object BammetricsReportPage {
def alignmentSummaryValues(summary: SummaryDb,
runId: Int,
......@@ -99,7 +103,8 @@ object BammetricsReportPage {
else None
val statsPaths = fields.map(x => x -> List("clipping", "general", x)).toMap
val clippingTableResults = summary.getStatsForLibraries(runId, "bammetrics", "bamstats", sampleId, statsPaths)
val clippingTableResults =
summary.getStatsForLibraries(runId, "bammetrics", "bamstats", sampleId, statsPaths)
Map(
"clippingPlotTables" -> clippingPlotTables,
"clippingTableResults" -> clippingTableResults,
......@@ -117,7 +122,8 @@ object BammetricsReportPage {
allLibraries: Seq[Library],
sampleId: Option[Int],
libId: Option[Int],
fields: List[String] = List("mean_insert_size", "standard_deviation", "median_insert_size"),
fields: List[String] =
List("mean_insert_size", "standard_deviation", "median_insert_size"),
sampleLevel: Boolean = false,
showPlot: Boolean = false,
showIntro: Boolean = true,
......@@ -133,7 +139,11 @@ object BammetricsReportPage {
else None
val statsPaths = fields.map(x => x -> List("metrics", x.toUpperCase)).toMap
val insertSizeTableResults = summary.getStatsForLibraries(runId, "bammetrics", "CollectInsertSizeMetrics", sampleId, statsPaths)
val insertSizeTableResults = summary.getStatsForLibraries(runId,
"bammetrics",
"CollectInsertSizeMetrics",
sampleId,
statsPaths)
Map(
"insertSizePlotTables" -> insertSizePlotTables,
"insertSizeTableResults" -> insertSizeTableResults,
......@@ -150,7 +160,10 @@ object BammetricsReportPage {
allLibraries: Seq[Library],
sampleId: Option[Int],
libId: Option[Int],
fields: List[String] = List("PF_ALIGNED_BASES", "MEDIAN_5PRIME_BIAS", "MEDIAN_3PRIME_BIAS", "MEDIAN_5PRIME_TO_3PRIME_BIAS"),
fields: List[String] = List("PF_ALIGNED_BASES",
"MEDIAN_5PRIME_BIAS",
"MEDIAN_3PRIME_BIAS",
"MEDIAN_5PRIME_TO_3PRIME_BIAS"),
sampleLevel: Boolean = false,
showPlot: Boolean = false,
showIntro: Boolean = true,
......@@ -166,7 +179,8 @@ object BammetricsReportPage {
else None
val statsPaths = fields.map(x => x -> List("metrics", x.toUpperCase)).toMap
val rnaHistogramTableResults = summary.getStatsForLibraries(runId, "bammetrics", "rna", sampleId, statsPaths)
val rnaHistogramTableResults =
summary.getStatsForLibraries(runId, "bammetrics", "rna", sampleId, statsPaths)
Map(
"rnaHistogramPlotTables" -> rnaHistogramPlotTables,
"rnaHistogramTableResults" -> rnaHistogramTableResults,
......@@ -183,7 +197,20 @@ object BammetricsReportPage {
allLibraries: Seq[Library],
sampleId: Option[Int],
libId: Option[Int],
fields: List[String] = List("mean_coverage", "pct_5x", "pct_10x", "pct_15x", "pct_20x", "pct_25x", "pct_30x", "pct_40x", "pct_50x", "pct_60x", "pct_70x", "pct_80x", "pct_90x", "pct_100x"),
fields: List[String] = List("mean_coverage",
"pct_5x",
"pct_10x",
"pct_15x",
"pct_20x",
"pct_25x",
"pct_30x",
"pct_40x",
"pct_50x",
"pct_60x",
"pct_70x",
"pct_80x",
"pct_90x",
"pct_100x"),
sampleLevel: Boolean = false,
showPlot: Boolean = false,
showIntro: Boolean = true,
......@@ -199,7 +226,8 @@ object BammetricsReportPage {
else None
val statsPaths = fields.map(x => x -> List("metrics", x.toUpperCase)).toMap
val wgsHistogramTableResults = summary.getStatsForLibraries(runId, "bammetrics", "wgs", sampleId, statsPaths)
val wgsHistogramTableResults =
summary.getStatsForLibraries(runId, "bammetrics", "wgs", sampleId, statsPaths)
Map(
"wgsHistogramPlotTables" -> wgsHistogramPlotTables,
"wgsHistogramTableResults" -> wgsHistogramTableResults,
......@@ -210,5 +238,41 @@ object BammetricsReportPage {
"libId" -> libId
)
}
def covstatsPlotValues(summary: SummaryDb,
runId: Int,
sampleId: Option[Int],
libId: Option[Int],
target: Option[String],
metricsTag: String = "bammetrics",
fields: List[String] = List("mean",
"median",
"max",
"horizontal",
"frac_min_10x",
"frac_min_20x",
"frac_min_30x",
"frac_min_40x",
"frac_min_50x")): Map[String, Any] = {
val moduleName = target.get + "_cov_stats"
val plotFile: Option[Schema.File] = Await.result(
summary.getFile(runId,
PipelineName(metricsTag),
ModuleName(moduleName),
sampleId.map(SampleId).get,
libId.map(LibraryId).getOrElse(NoLibrary),
"plot"),
Duration.Inf
)
val statsPaths = fields.map(x => x -> List("coverage", "_all", x)).toMap
val values: Map[String, Option[Any]] = summary.getStatKeys(
runId,
PipelineName(metricsTag),
ModuleName(moduleName),
sampleId.map(SampleId).get,
libId.map(LibraryId).getOrElse(NoLibrary),
statsPaths)
Map("plotFile" -> plotFile, "values" -> values,
"target" -> target,
"metricsTag" -> metricsTag)
}
}
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala
View file @ e5b7192d
......@@ -53,15 +53,16 @@ object FlexiprepReport extends ReportBuilder {
/** Index page for a flexiprep report */
def indexPage: Future[ReportPage] = {
val flexiprepPageSummaries = this.flexiprepPageSummaries(summary, sampleId.get, libId.get)
this.flexiprepPage(flexiprepPageSummaries).map {
page =>
this.flexiprepPage(flexiprepPageSummaries).map { page =>
ReportPage(
Nil,
List(
"Report" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFront.ssp")
) ::: page.sections,
Map())
}}
}
}
/** Generate a QC report page for 1 single library, sampleId and libId must be defined in the arguments */
def flexiprepPageSummaries(summary: SummaryDb,
sampleId: Int,
......@@ -73,7 +74,7 @@ object FlexiprepReport extends ReportBuilder {
sampleId,
libId,
multisample = false)
val flexiprepBaseSummary: Map[String,Any] = FlexiprepBaseSummary.values(summary,
val flexiprepBaseSummary: Map[String, Any] = FlexiprepBaseSummary.values(summary,
runId,
samples,
libraries,
......@@ -81,8 +82,7 @@ object FlexiprepReport extends ReportBuilder {
libId,
multisample = false)
Map("flexiprepReadSummary" -> flexiprepReadSummary,
"flexiprepBaseSummary" -> flexiprepBaseSummary
)
"flexiprepBaseSummary" -> flexiprepBaseSummary)
}
def flexiprepPage(summaries: Map[String, Map[String, Any]]): Future[ReportPage] = {
......
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
View file @ e5b7192d
......@@ -345,10 +345,10 @@ object GearsReport extends MultisampleReportBuilder {
val flexiprepReportPage =
if (flexiprepExecuted) {
val flexiprepPageSummaries = FlexiprepReport.flexiprepPageSummaries(summary,sampleId,libId)
val flexiprepPageSummaries =
FlexiprepReport.flexiprepPageSummaries(summary, sampleId, libId)
Some("QC" -> FlexiprepReport.flexiprepPage(flexiprepPageSummaries))
}
else None
} else None
val centrifugePageAllMappingsKronaPlot = GearsKronaPlot.values(summary,
runId,
......
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala
View file @ e5b7192d
......@@ -14,9 +14,18 @@
*/
package nl.lumc.sasc.biopet.pipelines.mapping
import nl.lumc.sasc.biopet.core.report.{MultisampleReportBuilder, ReportBuilderExtension, ReportPage, ReportSection}
import nl.lumc.sasc.biopet.core.report.{
MultisampleReportBuilder,
ReportBuilderExtension,
ReportPage,
ReportSection
}
import nl.lumc.sasc.biopet.pipelines.bammetrics.{BammetricsReport, BammetricsReportPage}
import nl.lumc.sasc.biopet.pipelines.flexiprep.{FlexiprepReadSummary,FlexiprepBaseSummary, FlexiprepReport}
import nl.lumc.sasc.biopet.pipelines.flexiprep.{
FlexiprepReadSummary,
FlexiprepBaseSummary,
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._
......@@ -137,16 +146,58 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
sampleLevel = true,
showPlot = true,
showTable = false)
val clippingReportValues = BammetricsReportPage.clippingValues(summary, runId, samples,
libraries, sampleId, libId, sampleLevel = true, showPlot = true, showTable = false)
val insertSizeReportValues = BammetricsReportPage.insertSizeValues(summary, runId, samples,
libraries, sampleId, libId, sampleLevel = true, showPlot = true, showTable = false)
val wgsHistogramReportValues = BammetricsReportPage.wgsHistogramValues(summary, runId, samples,
libraries, sampleId, libId, sampleLevel = true, showPlot = true, showTable = false)
val rnaHistogramReportValues = BammetricsReportPage.rnaHistogramValues(summary, runId, samples,
libraries, sampleId, libId, sampleLevel = true, showPlot = true, showTable = false)
val flexiprepReadSummary = FlexiprepReadSummary.values(summary, runId, samples, libraries, sampleId, libId, showPlot = true, showTable = false)
val flexiprepBaseSummary = FlexiprepBaseSummary.values(summary, runId, samples, libraries, sampleId, libId, showPlot = true, showTable = false)
val clippingReportValues = BammetricsReportPage.clippingValues(summary,
runId,
samples,
libraries,
sampleId,
libId,
sampleLevel = true,
showPlot = true,
showTable = false)
val insertSizeReportValues = BammetricsReportPage.insertSizeValues(summary,
runId,
samples,
libraries,
sampleId,
libId,
sampleLevel = true,
showPlot = true,
showTable = false)
val wgsHistogramReportValues = BammetricsReportPage.wgsHistogramValues(summary,
runId,
samples,
libraries,
sampleId,
libId,
sampleLevel = true,
showPlot = true,
showTable = false)
val rnaHistogramReportValues = BammetricsReportPage.rnaHistogramValues(summary,
runId,
samples,
libraries,
sampleId,
libId,
sampleLevel = true,
showPlot = true,
showTable = false)
val flexiprepReadSummary = FlexiprepReadSummary.values(summary,
runId,
samples,
libraries,
sampleId,
libId,
showPlot = true,
showTable = false)
val flexiprepBaseSummary = FlexiprepBaseSummary.values(summary,
runId,
samples,
libraries,
sampleId,
libId,
showPlot = true,
showTable = false)
Future {
ReportPage(
List("Samples" -> generateSamplesPage(pageArgs)) ++
......@@ -248,18 +299,49 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
summary.getStatsSize(runId, "flexiprep", sample = sampleId, mustHaveLibrary = true),
Duration.Inf) >= 1
val centrifugeAllMappingsReportValues = GearsKronaPlot.values(summary, runId, "gearscentrifuge",
"centrifuge_report", samples, libraries, sampleId, libId, Some("centrifuge"))
val centrifugeUniqueMappingsReportValues = GearsKronaPlot.values(summary, runId, "gearscentrifuge",
"centrifuge_unique_report", samples, libraries, sampleId, libId)
val dustbinAnalysisReportValues = GearsKronaPlot.values(summary, runId, "gearskraken", "krakenreport",
samples, libraries, sampleId, libId)
val alignmentSummaryReportValues = BammetricsReportPage.alignmentSummaryValues(summary, runId,
samples, libraries, sampleId, libId, showPlot = true)
val preprocessingReportValues = BammetricsReportPage.alignmentSummaryValues(summary, runId,
samples, libraries, sampleId, libId, sampleLevel = true)
val flexiprepReadSummary = FlexiprepReadSummary.values(summary, runId, samples, libraries, sampleId, libId)
val flexiprepBaseSummary = FlexiprepBaseSummary.values(summary, runId, samples, libraries, sampleId, libId)
val centrifugeAllMappingsReportValues = GearsKronaPlot.values(summary,
runId,
"gearscentrifuge",
"centrifuge_report",
samples,
libraries,
sampleId,
libId,
Some("centrifuge"))
val centrifugeUniqueMappingsReportValues = GearsKronaPlot.values(summary,
runId,
"gearscentrifuge",
"centrifuge_unique_report",
samples,
libraries,
sampleId,
libId)
val dustbinAnalysisReportValues = GearsKronaPlot.values(summary,
runId,
"gearskraken",
"krakenreport",
samples,
libraries,
sampleId,
libId)
val alignmentSummaryReportValues = BammetricsReportPage.alignmentSummaryValues(summary,
runId,
samples,
libraries,
sampleId,
libId,
showPlot = true)
val preprocessingReportValues = BammetricsReportPage.alignmentSummaryValues(summary,
runId,
samples,
libraries,
sampleId,
libId,
sampleLevel = true)
val flexiprepReadSummary =
FlexiprepReadSummary.values(summary, runId, samples, libraries, sampleId, libId)
val flexiprepBaseSummary =
FlexiprepBaseSummary.values(summary, runId, samples, libraries, sampleId, libId)
Future {
ReportPage(
......@@ -268,7 +350,9 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
(if (centrifugeExecuted)
List(
"Centrifuge analysis" -> Future.successful(ReportPage(
List("Non-unique" -> Future.successful(ReportPage(
List(
"Non-unique" -> Future.successful(
ReportPage(
List(),
List("All mappings" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
......@@ -286,7 +370,8 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
"Dustbin analysis" -> Future.successful(
ReportPage(List(),
List("Krona Plot" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp", dustbinAnalysisReportValues)),
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
dustbinAnalysisReportValues)),
Map())))
else Nil),
List(
......@@ -300,9 +385,11 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
(if (flexiprepExecuted)
List(
"QC reads" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp", flexiprepReadSummary),
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp",
flexiprepReadSummary),
"QC bases" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp", flexiprepBaseSummary)
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp",
flexiprepBaseSummary)
)
else Nil),
args
......@@ -310,9 +397,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
}
/** Library page */
def libraryPage(sampleId: Int,
libId: Int,
args: Map[String, Any]): Future[ReportPage] = {
def libraryPage(sampleId: Int, libId: Int, args: Map[String, Any]): Future[ReportPage] = {
val krakenExecuted = Await.result(summary.getStatsSize(runId,
"gearskraken",
"krakenreport",
......@@ -332,12 +417,12 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
sample = sampleId,
mustHaveLibrary = true),
Duration.Inf) >= 1
val flexiprepPageSummaries = FlexiprepReport.flexiprepPageSummaries(summary, sampleId, libId)
Future {
ReportPage(
("Alignment" -> BammetricsReport.bamMetricsPage(summary, Some(sampleId), Some(libId))) ::
(if (flexiprepExecuted)
List("QC" -> FlexiprepReport.flexiprepPage(summary, sampleId, libId))
List("QC" -> FlexiprepReport.flexiprepPage(flexiprepPageSummaries))
else Nil) :::
(if (centrifugeExecuted)
List("Centrifuge analysis" -> Future.successful(ReportPage(
......@@ -352,7 +437,8 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
Map("summaryStatsTag" -> "centrifuge_unique_report"))),
Map("summaryModuleTag" -> "gearscentrifuge", "centrifugeTag" -> Some("centrifuge"))
)))
else Nil) ::: (if (krakenExecuted)
else
Nil) ::: (if (krakenExecuted)
List(
"Dustbin analysis" -> Future.successful(
ReportPage(List(),
......
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