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Commit 763f8f4d authored by Ruben Vorderman's avatar Ruben Vorderman
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Gearsreport completely defutured

parent 97661f8f
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Showing with 223 additions and 165 deletions
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala
View file @ 763f8f4d
......@@ -16,20 +16,22 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep
import java.io.{File, PrintWriter}
import nl.lumc.sasc.biopet.core.report.{
ReportBuilder,
ReportBuilderExtension,
ReportPage,
ReportSection
}
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.report.{ReportBuilder, ReportBuilderExtension, ReportPage, ReportSection}
import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport.runId
import nl.lumc.sasc.biopet.utils.rscript.StackedBarPlot
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.Sample
import nl.lumc.sasc.biopet.utils.summary.db.Schema.Library
import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._
import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._
import scala.collection.mutable
import scala.collection.mutable.{ArrayBuffer, ListBuffer}
import scala.concurrent.{Await, Future}
import scala.collection.mutable.ArrayBuffer
import scala.concurrent.duration.Duration
import scala.concurrent.{Await, Future}
class FlexiprepReport(val parent: Configurable) extends ReportBuilderExtension {
def builder = FlexiprepReport
......@@ -84,30 +86,31 @@ object FlexiprepReport extends ReportBuilder {
name -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFastQcPlot.ssp",
Map("plot" -> tag))
}
/**
* Generates the lines for readSummaryPlot
* @param read Must give "R1" or "R2"
* @param summary Summary class
* @param sampleId Default selects all samples, when given plot is limits on given sample
*/
def readSummaryPlotLines(read: String,
summary: SummaryDb,
sampleId: Option[Int] = None) : Seq[String] = {
/**
* Generates the lines for readSummaryPlot
* @param read Must give "R1" or "R2"
* @param summary Summary class
* @param sampleId Default selects all samples, when given plot is limits on given sample
*/
def readSummaryPlotLines(read: String,
summary: SummaryDb,
sampleId: Option[Int] = None): Seq[String] = {
val seqstatPaths = Map("num_total" -> List("reads", "num_total"))
val seqstatStats =
summary.getStatsForLibraries(runId, "flexiprep", "seqstat_" + read, keyValues = seqstatPaths)
val seqstatQcStats = summary.getStatsForLibraries(runId,
"flexiprep",
"seqstat_" + read + "_qc",
keyValues = seqstatPaths)
"flexiprep",
"seqstat_" + read + "_qc",
keyValues = seqstatPaths)
val clippingPaths = Map(
"num_reads_discarded_too_short" -> List("num_reads_discarded_too_short"),
"num_reads_discarded_too_long" -> List("num_reads_discarded_too_long"))
val clippingStats = summary.getStatsForLibraries(runId,
"flexiprep",
"clipping_" + read,
keyValues = clippingPaths)
"flexiprep",
"clipping_" + read,
keyValues = clippingPaths)
val trimmingPaths = Map("num_reads_discarded" -> List("num_reads_discarded_" + read))
val trimmingStats =
......@@ -155,8 +158,7 @@ def readSummaryPlotLines(read: String,
def readSummaryPlot(outputDir: File,
prefix: String,
read: String,
summaryPlotLines: Seq[String])
: Unit = {
summaryPlotLines: Seq[String]): Unit = {
val tsvFile = new File(outputDir, prefix + ".tsv")
val pngFile = new File(outputDir, prefix + ".png")
val tsvWriter = new PrintWriter(tsvFile)
......@@ -181,19 +183,17 @@ def readSummaryPlotLines(read: String,
* @param summary Summary class
* @param sampleId Default selects all samples, when given plot is limits on given sample
*/
def baseSummaryPlotLines (read: String,
summary: SummaryDb,
sampleId: Option[Int] = None): Seq[String] = {
def baseSummaryPlotLines(read: String,
summary: SummaryDb,
sampleId: Option[Int] = None): Seq[String] = {
val statsPaths = Map("num_total" -> List("bases", "num_total"))
val seqstatStats =
summary.getStatsForLibraries(runId, "flexiprep", "seqstat_" + read, keyValues = statsPaths)
val seqstatQcStats = summary.getStatsForLibraries(runId,
"flexiprep",
"seqstat_" + read + "_qc",
keyValues = statsPaths)
"flexiprep",
"seqstat_" + read + "_qc",
keyValues = statsPaths)
val libraries =
Await.result(summary.getLibraries(runId = runId, sampleId = sampleId), Duration.Inf)
......@@ -215,7 +215,7 @@ def readSummaryPlotLines(read: String,
summaryPlotLines += sb.toString
}
summaryPlotLines
summaryPlotLines
}
/**
......@@ -224,7 +224,7 @@ def readSummaryPlotLines(read: String,
* @param prefix prefix for tsv and png file
* @param read Must give "R1" or "R2"
* @param summaryPlotLines A sequence of strings written to the summary tsv
*/
*/
def baseSummaryPlot(outputDir: File,
prefix: String,
read: String,
......@@ -234,7 +234,7 @@ def readSummaryPlotLines(read: String,
val tsvWriter = new PrintWriter(tsvFile)
tsvWriter.println("Library\tAfter_QC\tDiscarded")
for (line <- summaryPlotLines){
for (line <- summaryPlotLines) {
tsvWriter.println(line)
}
......@@ -288,8 +288,11 @@ object FlexiprepReadSummary {
val clipCount = settings.count(_._2.getOrElse("skip_clip", None).contains(false))
val librariesCount = libraries.size
val summaryPlotLinesR1 = if (showPlot) FlexiprepReport.readSummaryPlotLines("R1", summary, sampleId = sampleId)
val summaryPlotlinesR2 = if (showPlot && paired) FlexiprepReport.readSummaryPlotLines("R2", summary, sampleId = sampleId)
val summaryPlotLinesR1 =
if (showPlot) FlexiprepReport.readSummaryPlotLines("R1", summary, sampleId = sampleId)
val summaryPlotlinesR2 =
if (showPlot && paired)
FlexiprepReport.readSummaryPlotLines("R2", summary, sampleId = sampleId)
val seqstatPaths = Map("num_total" -> List("reads", "num_total"))
val clippingPaths = Map(
......@@ -306,7 +309,6 @@ object FlexiprepReadSummary {
summary.getStatsForLibraries(runId, "flexiprep", "seqstat_R1", sampleId, trimmingPaths)
Map(
"summary" -> summary,
"runId" -> runId,
"sampleId" -> sampleId,
"libId" -> libId,
......@@ -337,24 +339,38 @@ object FlexiprepBaseSummary {
showPlot: Boolean = false,
showTable: Boolean = true,
showIntro: Boolean = true,
multisample: Boolean = true): Map[String,Any] = {
multisample: Boolean = true): Map[String, Any] = {
val samples = sampleId.map(id => allSamples.filter(_.id == id)).getOrElse(allSamples)
val libraries = libId.map(id => allLibraries.filter(_.id == id)).getOrElse(allLibraries)
val librariesCount = libraries.size
val settings = summary.getSettingsForLibraries(runId, "flexiprep", keyValues = Map(
"skip_trim" -> List("skip_trim"), "skip_clip" -> List("skip_clip"), "paired" -> List("paired")))
val settings = summary.getSettingsForLibraries(runId,
"flexiprep",
keyValues =
Map("skip_trim" -> List("skip_trim"),
"skip_clip" -> List("skip_clip"),
"paired" -> List("paired")))
settings.count(_._2.getOrElse("skip_trim", None) == Some(true))
val trimCount = settings.count(_._2.getOrElse("skip_trim", None) == Some(false))
val clipCount = settings.count(_._2.getOrElse("skip_clip", None) == Some(false))
val paired: Boolean = if (sampleId.isDefined && libId.isDefined)
summary.getSettingKeys(runId, "flexiprep", NoModule, SampleId(sampleId.get), LibraryId(libId.get), keyValues = Map("paired" -> List("paired"))).getOrElse("paired", None) == Some(true)
else settings.count(_._2.getOrElse("paired", None) == Some(true)) >= 1
val paired: Boolean =
if (sampleId.isDefined && libId.isDefined)
summary
.getSettingKeys(runId,
"flexiprep",
NoModule,
SampleId(sampleId.get),
LibraryId(libId.get),
keyValues = Map("paired" -> List("paired")))
.getOrElse("paired", None) == Some(true)
else settings.count(_._2.getOrElse("paired", None) == Some(true)) >= 1
val summaryPlotLinesR1 = if (showPlot) FlexiprepReport.readSummaryPlotLines("R1", summary, sampleId = sampleId)
val summaryPlotlinesR2 = if (showPlot && paired) FlexiprepReport.readSummaryPlotLines("R2", summary, sampleId = sampleId)
val summaryPlotLinesR1 =
if (showPlot) FlexiprepReport.readSummaryPlotLines("R1", summary, sampleId = sampleId)
val summaryPlotlinesR2 =
if (showPlot && paired)
FlexiprepReport.readSummaryPlotLines("R2", summary, sampleId = sampleId)
val statsPaths = Map("num_total" -> List("bases", "num_total"))
......@@ -363,14 +379,21 @@ object FlexiprepBaseSummary {
val seqstatQCStats =
summary.getStatsForLibraries(runId, "flexiprep", "seqstat_R1_QC", sampleId, statsPaths)
Map(
"trimCount" -> trimCount,
"librariesCount" -> librariesCount,
"clipCount" -> clipCount,
"paired" -> paired,
"summaryPlotLinesR1" -> summaryPlotLinesR1,
"summaryPlotLinesR2" -> summaryPlotlinesR2
"runId" -> runId,
"sampleId" -> sampleId,
"libId" -> libId,
"showPlot" -> showPlot,
"settings" -> settings,
"samples" -> samples,
"libraries" -> libraries,
"trimCount" -> trimCount,
"clipCount" -> clipCount,
"librariesCount" -> librariesCount,
"seqstatStats" -> seqstatStats,
"seqstatQCStats" -> seqstatQCStats,
"summaryPlotLinesR1" -> summaryPlotLinesR1,
"summaryPlotLinesR2" -> summaryPlotlinesR2
)
}
}
\ No newline at end of file
}
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
View file @ 763f8f4d
......@@ -16,8 +16,17 @@ package nl.lumc.sasc.biopet.pipelines.gears
import java.io.File
import nl.lumc.sasc.biopet.core.report.{MultisampleReportBuilder, ReportBuilderExtension, ReportPage, ReportSection}
import nl.lumc.sasc.biopet.pipelines.flexiprep.{FlexiprepReadSummary, FlexiprepReport}
import nl.lumc.sasc.biopet.core.report.{
MultisampleReportBuilder,
ReportBuilderExtension,
ReportPage,
ReportSection
}
import nl.lumc.sasc.biopet.pipelines.flexiprep.{
FlexiprepBaseSummary,
FlexiprepReadSummary,
FlexiprepReport
}
import nl.lumc.sasc.biopet.pipelines.gears
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb
......@@ -67,54 +76,57 @@ object GearsReport extends MultisampleReportBuilder {
mustHaveSample = true) >= samples.size
val qiimeClosesOtuTable = summary.getFile(runId, "gears", key = "qiime_closed_otu_table")
val qiimeOpenOtuTable = summary.getFile(runId, "gears", key = "qiime_open_otu_table")
val centrifugePageAllMappingsKronaPlot = GearsKronaPlot.values(summary,
runId,
"centrifuge_report",
"centrifuge_report",
samples,
libraries,
sampleId,
libId,
Some("centrifuge"))
val centrifugePageUniqueMappingsKronaPlot = GearsKronaPlot.values(summary,
runId,
"centrifuge_unique_report",
"centrifuge_unique_report",
samples,
libraries,
sampleId,
libId)
val centrifugePage =
if (centrifugeExecuted)
Some(
"Centrifuge analysis" -> Future.successful(ReportPage(
List("Non-unique" ->
Future.successful(ReportPage(
List(),
List("All mappings" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
GearsKronaPlot.values(summary,
runId,
"centrifuge_report",
"centrifuge_report",
samples,
libraries,
sampleId,
libId,
Some("centrifuge"))
)),
Map()
))),
List(
"Non-unique" ->
Future.successful(
ReportPage(
List(),
List("All mappings" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
centrifugePageAllMappingsKronaPlot)),
Map()
))),
List("Unique mappings" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
Map("summaryStatsTag" -> "centrifuge_unique_report"))),
centrifugePageUniqueMappingsKronaPlot)),
Map("summaryModuleTag" -> "gearscentrifuge", "centrifugeTag" -> Some("centrifuge"))
)))
else None
val krakenPageKronaPlot = GearsKronaPlot
.values(summary, runId, "Krona", "krakenkrona", samples, libraries, sampleId, libId)
val krakenPage =
if (krakenExecuted)
Some(
"Kraken analysis" -> Future.successful(ReportPage(
List(),
List(
"Krona plot" -> Future.successful(
"Kraken analysis" -> Future.successful(
ReportPage(
List(),
List("Krona plot" -> Future.successful(
ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
GearsKronaPlot
.values(summary,
runId,
"Krona",
"krakenkrona",
samples,
libraries,
sampleId,
libId)))),
Map()
)))
krakenPageKronaPlot))),
Map()
)))
else None
val qiimeClosedPage =
......@@ -141,7 +153,10 @@ object GearsReport extends MultisampleReportBuilder {
)))
else None
val flexiprepReadSummary = FlexiprepReadSummary.values(summary,runId,samples,libraries,sampleId,libId, true, false)
val flexiprepReadSummary =
FlexiprepReadSummary.values(summary, runId, samples, libraries, sampleId, libId, true, false)
val flexiprepBaseSummary =
FlexiprepBaseSummary.values(summary, runId, samples, libraries, sampleId, libId, true, false)
Future {
ReportPage(
List(centrifugePage, krakenPage, qiimeClosedPage, qiimeOpenPage).flatten ::: List(
......@@ -154,7 +169,7 @@ object GearsReport extends MultisampleReportBuilder {
flexiprepReadSummary),
"QC bases" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp",
Map("showPlot" -> true, "showTable" -> false))
flexiprepBaseSummary)
),
pageArgs
)
......@@ -186,51 +201,55 @@ object GearsReport extends MultisampleReportBuilder {
val qiimeOpenOtuTable = Await.result(
summary.getFile(runId, "gearssingle", NoModule, sampleId, NoLibrary, "qiime_open_otu_table"),
Duration.Inf)
val centrifugePageAllMappingsKronaPlot = GearsKronaPlot.values(summary,
runId,
"centrifuge_report",
"centrifuge_report",
samples,
libraries,
sampleId,
libId,
Some("centrifuge"))
val centrifugePageUniqueMappingsKronaPlot = GearsKronaPlot.values(summary,
runId,
"centrifuge_unique_report",
"centrifuge_unique_report",
samples,
libraries,
sampleId,
libId)
val gearsCentrifugePage = if (centrifugeExecuted) {
Some(
"Centrifuge analysis" -> Future.successful(ReportPage(
List("Non-unique" -> Future.successful(ReportPage(
List(),
List("All mappings" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
GearsKronaPlot.values(summary,
runId,
"centrifuge_report",
"centrifuge_report",
samples,
libraries,
sampleId,
libId,
Some("centrifuge"))
)),
Map()
))),
List(
"Non-unique" -> Future.successful(
ReportPage(
List(),
List("All mappings" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
centrifugePageAllMappingsKronaPlot
)),
Map()
))),
List("Unique mappings" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
Map("summaryStatsTag" -> "centrifuge_unique_report"))),
centrifugePageUniqueMappingsKronaPlot)),
Map("summaryModuleTag" -> "gearscentrifuge", "centrifugeTag" -> Some("centrifuge"))
)))
} else None
val krakenPageKronaPlot = GearsKronaPlot
.values(summary, runId, "Krona", "krakenkrona", samples, libraries, sampleId, libId)
val krakenAnalysisPage =
if (krakenExecuted)
Some(
"Kraken analysis" -> Future.successful(ReportPage(
List(),
List(
"Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
GearsKronaPlot
.values(summary,
runId,
"Krona",
"krakenkrona",
samples,
libraries,
sampleId,
libId))),
Map()
)))
"Kraken analysis" -> Future.successful(
ReportPage(
List(),
List("Krona plot" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
krakenPageKronaPlot)),
Map()
)))
else None
val qiimeClosesOtuTablePage =
......@@ -257,6 +276,10 @@ object GearsReport extends MultisampleReportBuilder {
)))
else None
val flexiprepReadSummary =
FlexiprepReadSummary.values(summary, runId, samples, libraries, sampleId)
val flexiprepBaseSummary =
FlexiprepBaseSummary.values(summary, runId, samples, libraries, sampleId)
Future {
ReportPage(
subPages =
......@@ -268,9 +291,11 @@ object GearsReport extends MultisampleReportBuilder {
),
sections = List(
"QC reads" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"),
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp",
flexiprepReadSummary),
"QC bases" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp")
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp",
flexiprepBaseSummary)
),
args = args
)
......@@ -308,51 +333,56 @@ object GearsReport extends MultisampleReportBuilder {
val flexiprepReportPage =
if (flexiprepExecuted) Some("QC" -> FlexiprepReport.flexiprepPage) else None
val centrifugePageAllMappingsKronaPlot = GearsKronaPlot.values(summary,
runId,
"centrifuge_report",
"centrifuge_report",
samples,
libraries,
sampleId,
libId,
Some("centrifuge"))
val centrifugePageUniqueMappingsKronaPlot = GearsKronaPlot.values(summary,
runId,
"centrifuge_unique_report",
"centrifuge_unique_report",
samples,
libraries,
sampleId,
libId)
val centrifugeReportPage =
if (centrifugeExecuted)
Some(
"Centrifuge analysis" -> Future.successful(ReportPage(
List("Non-unique" -> Future.successful(ReportPage(
List(),
List("All mappings" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
GearsKronaPlot.values(summary,
runId,
"centrifuge_report",
"centrifuge_report",
samples,
libraries,
sampleId,
libId,
Some("centrifuge"))
)),
Map()
))),
List(
"Non-unique" -> Future.successful(
ReportPage(
List(),
List("All mappings" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
centrifugePageAllMappingsKronaPlot
)),
Map()
))),
List("Unique mappings" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
Map("summaryStatsTag" -> "centrifuge_unique_report"))),
centrifugePageUniqueMappingsKronaPlot)),
Map("summaryModuleTag" -> "gearscentrifuge", "centrifugeTag" -> Some("centrifuge"))
)))
else None
val krakenPageKronaPlot = GearsKronaPlot
.values(summary, runId, "Krona", "krakenkrona", samples, libraries, sampleId, libId)
val krakenAnalysisPage =
if (krakenExecuted)
Some(
"Kraken analysis" -> Future.successful(ReportPage(
List(),
List(
"Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
GearsKronaPlot
.values(summary,
runId,
"Krona",
"krakenkrona",
samples,
libraries,
sampleId,
libId))),
Map()
)))
"Kraken analysis" -> Future.successful(
ReportPage(
List(),
List("Krona plot" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
krakenPageKronaPlot)),
Map()
)))
else None
val qiimeClosesOtuTablePage =
......@@ -375,7 +405,10 @@ object GearsReport extends MultisampleReportBuilder {
"/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp")),
Map("biomFile" -> new File(qiimeOpenOtuTable.get.path)))))
else None
val flexiprepReadSummary =
FlexiprepReadSummary.values(summary, runId, samples, libraries, sampleId)
val flexiprepBaseSummary =
FlexiprepBaseSummary.values(summary, runId, samples, libraries, sampleId)
Future {