diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
index 8bf19381ed25f995fe73bc507f5029830a3b1cb0..ffad82b7e2f5c4ab3df0f886516bcc7fb83af45c 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
@@ -121,10 +121,7 @@ class Gentrap(val root: Configurable) extends QScript
lazy val fragmentsPerExon = if (expMeasures.contains(ExpMeasures.FragmentsPerExon))
Some(new FragmentsPerExon(this)) else None
- lazy val basesPerGene = if (expMeasures.contains(ExpMeasures.BasesPerGene))
- Some(new BasesPerGene(this)) else None
-
- lazy val basesPerExon = if (expMeasures.contains(ExpMeasures.BasesPerExon))
+ lazy val baseCounts = if (expMeasures.contains(ExpMeasures.BaseCounts))
Some(new FragmentsPerExon(this)) else None
lazy val cufflinksBlind = if (expMeasures.contains(ExpMeasures.CufflinksBlind))
@@ -136,7 +133,7 @@ class Gentrap(val root: Configurable) extends QScript
lazy val cufflinksStrict = if (expMeasures.contains(ExpMeasures.CufflinksStrict))
Some(new CufflinksStrict(this)) else None
- def executedMeasures = (fragmentsPerGene :: fragmentsPerExon :: basesPerGene :: basesPerExon :: cufflinksBlind ::
+ def executedMeasures = (fragmentsPerGene :: fragmentsPerExon :: baseCounts :: cufflinksBlind ::
cufflinksGuided :: cufflinksStrict :: Nil).flatten
/** Whether to do simple variant calling on RNA or not */
@@ -232,7 +229,7 @@ object Gentrap extends PipelineCommand {
/** Enumeration of available expression measures */
object ExpMeasures extends Enumeration {
- val FragmentsPerGene, FragmentsPerExon, BasesPerGene, BasesPerExon, CufflinksStrict, CufflinksGuided, CufflinksBlind = Value
+ val FragmentsPerGene, FragmentsPerExon, BaseCounts, CufflinksStrict, CufflinksGuided, CufflinksBlind = Value
}
/** Enumeration of available strandedness */
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/BaseCounts.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/BaseCounts.scala
new file mode 100644
index 0000000000000000000000000000000000000000..7a56733ea8ec669436c392f91ddc9ec0222ec2c1
--- /dev/null
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/BaseCounts.scala
@@ -0,0 +1,30 @@
+package nl.lumc.sasc.biopet.pipelines.gentrap.measures
+
+import nl.lumc.sasc.biopet.core.annotations.AnnotationRefFlat
+import nl.lumc.sasc.biopet.extensions.tools.BaseCounter
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.queue.QScript
+
+/**
+ * Created by pjvan_thof on 1/12/16.
+ */
+class BaseCounts(val root: Configurable) extends QScript with Measurement with AnnotationRefFlat {
+
+ def mergeArgs = MergeArgs(List(1), 2, numHeaderLines = 1, fallback = "0")
+
+ /** Pipeline itself */
+ def biopetScript(): Unit = {
+ val jobs = bamFiles.map { case (id, file) =>
+ val baseCounter = new BaseCounter(this)
+ baseCounter.bamFile = file
+ baseCounter.outputDir = new File(outputDir, id)
+ baseCounter.prefix = id
+ baseCounter.refFlat = annotationRefFlat
+ add(baseCounter)
+ id -> baseCounter
+ }
+
+ //TODO: merges
+ //TODO heatmaps
+ }
+}
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/BasesPerExon.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/BasesPerExon.scala
deleted file mode 100644
index d0feb6c8b2b9fc4c440d3ecfae601e5c3d9337a6..0000000000000000000000000000000000000000
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/BasesPerExon.scala
+++ /dev/null
@@ -1,13 +0,0 @@
-package nl.lumc.sasc.biopet.pipelines.gentrap.measures
-
-import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.queue.QScript
-
-/**
- * Created by pjvan_thof on 1/12/16.
- */
-class BasesPerExon(val root: Configurable) extends QScript with Measurement {
- def bamToCountFile(id: String, bamFile: File): (String, File) = ???
-
- def mergeArgs = MergeArgs(List(1), 2, numHeaderLines = 1, fallback = "0")
-}
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/BasesPerGene.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/BasesPerGene.scala
deleted file mode 100644
index d2650362f471088c2e8248974022dcb960a3e895..0000000000000000000000000000000000000000
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/BasesPerGene.scala
+++ /dev/null
@@ -1,14 +0,0 @@
-package nl.lumc.sasc.biopet.pipelines.gentrap.measures
-
-import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.queue.QScript
-
-/**
- * Created by pjvan_thof on 1/12/16.
- */
-class BasesPerGene(val root: Configurable) extends QScript with Measurement {
- //TODO: splitting on strand if strandspecific
- def bamToCountFile(id: String, bamFile: File): (String, File) = ???
-
- def mergeArgs = MergeArgs(List(1), 2, numHeaderLines = 1, fallback = "0")
-}
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/CufflinksMeasurement.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/CufflinksMeasurement.scala
index 1a9116c12d662ecca1de719f699ef72bac32fcee..229d78e6581a2627337ea6dd87d1378e219cc0e7 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/CufflinksMeasurement.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/CufflinksMeasurement.scala
@@ -15,25 +15,25 @@ trait CufflinksMeasurement extends QScript with Measurement {
cufflinks
}
- private var isoFormFiles: List[File] = Nil
-
- def bamToCountFile(id: String, bamFile: File): (String, File) = {
- val cufflinks = makeCufflinksJob(id, bamFile)
- add(cufflinks)
-
- isoFormFiles :+= cufflinks.outputIsoformsFpkm
-
- id -> cufflinks.outputGenesFpkm
+ def biopetScript(): Unit = {
+ val jobs = bamFiles.map { case (id, file) =>
+ val cufflinks = makeCufflinksJob(id, file)
+ add(cufflinks)
+ id -> cufflinks
+ }
+
+ addMergeTableJob(jobs.values.map(_.outputGenesFpkm).toList, mergeGenesFpkmTable)
+ addMergeTableJob(jobs.values.map(_.outputIsoformsFpkm).toList, mergeIsoFormFpkmTable)
+
+ addHeatmapJob(mergeGenesFpkmTable, genesFpkmHeatmap, "genes_fpkm")
+ addHeatmapJob(mergeIsoFormFpkmTable, isoFormFpkmHeatmap, "iso_form_fpkm")
}
- override def biopetScript(): Unit = {
- super.biopetScript()
-
- add(MergeTables(this, isoFormFiles, mergeIsoFormTable,
- mergeArgs.idCols, mergeArgs.valCol, mergeArgs.numHeaderLines, mergeArgs.fallback))
- }
+ def mergeGenesFpkmTable: File = new File(outputDir, s"$name.genes.fpkm.tsv")
+ def genesFpkmHeatmap: File = new File(outputDir, s"$name.genes.fpkm.png")
- def mergeIsoFormTable: File = new File(outputDir, s"$name.iso_form_table.tsv")
+ def mergeIsoFormFpkmTable: File = new File(outputDir, s"$name.iso_form.fpkm.tsv")
+ def isoFormFpkmHeatmap: File = new File(outputDir, s"$name.iso_form.fpkm.png")
def mergeArgs = MergeArgs(List(1, 7), 10, numHeaderLines = 1, fallback = "0.0")
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/FragmentsPerExon.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/FragmentsPerExon.scala
index 6f1268fcc5b677ad77dff37d76a457097c53669d..dbca36eed14d1203473b5b1d5d5ddaa33846733a 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/FragmentsPerExon.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/FragmentsPerExon.scala
@@ -7,7 +7,8 @@ import org.broadinstitute.gatk.queue.QScript
* Created by pjvan_thof on 1/12/16.
*/
class FragmentsPerExon(val root: Configurable) extends QScript with Measurement {
- def bamToCountFile(id: String, bamFile: File): (String, File) = ???
-
def mergeArgs = MergeArgs(List(1), 2, numHeaderLines = 1, fallback = "0")
+
+ /** Pipeline itself */
+ def biopetScript(): Unit = ???
}
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/FragmentsPerGene.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/FragmentsPerGene.scala
index a614f93e9249a9396555a6b2da85694309d75f6f..fd94996f6a797e6aee596a16b801e70cdcd87cc5 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/FragmentsPerGene.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/FragmentsPerGene.scala
@@ -25,4 +25,28 @@ class FragmentsPerGene(val root: Configurable) extends QScript with Measurement
}
def mergeArgs = MergeArgs(List(1), 2, numHeaderLines = 1, fallback = "0")
+
+ /** Pipeline itself */
+ def biopetScript(): Unit = {
+ val jobs = bamFiles.map { case (id, file) =>
+ //TODO: ID sorting job
+
+ val job = new HtseqCount(this)
+ job.inputAnnotation = annotationGtf
+ job.inputAlignment = file
+ job.output = new File(outputDir, s"$name.$id.counts")
+ job.format = Option("bam")
+ // We are forcing the sort order to be ID-sorted, since HTSeq-count often chokes when using position-sorting due
+ // to its buffer not being large enough.
+ //TODO: ID sorting job
+ //job.order = Option("name")
+ id -> job
+ }
+
+ addMergeTableJob(jobs.values.map(_.output).toList, mergedTable)
+ addHeatmapJob(mergedTable, heatmap, "fragments_per_gene")
+ }
+
+ def mergedTable = new File(outputDir, s"$name.fragments_per_gene.tsv")
+ def heatmap = new File(outputDir, s"$name.fragments_per_gene.png")
}
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/Measurement.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/Measurement.scala
index 1c5cc50b67bc93f561e9df7aaa36d1249f1eb707..f09cc09f6cf2fcfefcb55bb8c7296c9324514d2b 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/Measurement.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/Measurement.scala
@@ -1,7 +1,5 @@
package nl.lumc.sasc.biopet.pipelines.gentrap.measures
-import java.io.File
-
import nl.lumc.sasc.biopet.core.Reference
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.extensions.tools.MergeTables
@@ -27,15 +25,6 @@ trait Measurement extends SummaryQScript with Reference { qscript: QScript =>
/** Name of job, this is used as prefix for most of the files */
def name: String = this.getClass.getSimpleName.toLowerCase
- /** Locations of single bam count tables */
- lazy val countFiles: Map[String, File] = bamFiles.map { case (id, bamFile) => bamToCountFile(id, bamFile) }
-
- /** Location of merge count table */
- def mergedCountFile = new File(outputDir, s"$name.merged.tsv")
-
- /** Location of heatmap */
- def heatpMap = new File(outputDir, s"$name.heatmap.png")
-
/** Class to store args for MergeTables */
case class MergeArgs(idCols: List[Int], valCol: Int, numHeaderLines: Int = 0, fallback: String = "-")
@@ -47,27 +36,26 @@ trait Measurement extends SummaryQScript with Reference { qscript: QScript =>
require(bamFiles.nonEmpty)
}
- /** Pipeline itself */
- def biopetScript(): Unit = {
- add(MergeTables(this, countFiles.values.toList, mergedCountFile,
- mergeArgs.idCols, mergeArgs.valCol, mergeArgs.numHeaderLines, mergeArgs.fallback))
+ def addMergeTableJob(countFiles: List[File],
+ outputFile: File,
+ args: MergeArgs = mergeArgs): Unit = {
+ add(MergeTables(this, countFiles, outputFile,
+ args.idCols, args.valCol, args.numHeaderLines, args.fallback))
+ }
+ def addHeatmapJob(countTable: File, outputFile: File, name: String): Unit = {
val job = new PlotHeatmap(qscript)
- job.input = mergedCountFile
- job.output = heatpMap
+ job.input = countTable
+ job.output = outputFile
job.countType = Some(name)
add(job)
}
- /** This function should add the count table for each bamFile */
- def bamToCountFile(id: String, bamFile: File): (String, File)
-
/** Must return a map with used settings for this pipeline */
def summarySettings: Map[String, Any] = Map()
/** File to put in the summary for thie pipeline */
- def summaryFiles: Map[String, File] = Map("merged_table" -> mergedCountFile, "heatmap" -> heatpMap) ++
- bamFiles.map { case (id, file) => s"input_bam_$id" -> file }
+ def summaryFiles: Map[String, File] = Map() ++ bamFiles.map { case (id, file) => s"input_bam_$id" -> file }
/** Name of summary output file */
def summaryFile: File = new File(outputDir, s"$name.summary.json")