From 958e6ba4ff1dcd1d21ab77943a119e0c0e0a0444 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 20 Jan 2016 14:06:13 +0100
Subject: [PATCH] Move script and init to main trait
---
.../biopet/core/annotations/Annotations.scala | 20 +++++------
.../gentrap/measures/BasesPerExon.scala | 19 ++--------
.../gentrap/measures/BasesPerGene.scala | 20 +++--------
.../gentrap/measures/CufflinksBlind.scala | 19 ++--------
.../gentrap/measures/CufflinksGuided.scala | 19 ++--------
.../gentrap/measures/CufflinksStrict.scala | 19 ++--------
.../gentrap/measures/FragmentsPerExon.scala | 19 ++--------
.../gentrap/measures/FragmentsPerGene.scala | 19 ++--------
.../gentrap/measures/Measurement.scala | 35 ++++++++++++++++---
9 files changed, 63 insertions(+), 126 deletions(-)
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/annotations/Annotations.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/annotations/Annotations.scala
index 82d772fcd..d1300f020 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/annotations/Annotations.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/annotations/Annotations.scala
@@ -5,13 +5,13 @@ import nl.lumc.sasc.biopet.core.BiopetQScript.InputFile
import org.broadinstitute.gatk.queue.QScript
/**
- * Created by pjvan_thof on 1/12/16.
- */
+ * Created by pjvan_thof on 1/12/16.
+ */
trait AnnotationGtf extends BiopetQScript { qscript: QScript =>
/** GTF reference file */
lazy val annotationGtf: File = {
- val file: File = config("annotation_gtf")
- inputFiles :+ InputFile(file, config("annotation_gtf_md5"))
+ val file: File = config("annotation_gtf", freeVar = true)
+ inputFiles :+ InputFile(file, config("annotation_gtf_md5", freeVar = true))
file
}
}
@@ -19,8 +19,8 @@ trait AnnotationGtf extends BiopetQScript { qscript: QScript =>
trait AnnotationBed extends BiopetQScript { qscript: QScript =>
/** GTF reference file */
lazy val annotationBed: File = {
- val file: File = config("annotation_bed")
- inputFiles :+ InputFile(file, config("annotation_bed_md5"))
+ val file: File = config("annotation_bed", freeVar = true)
+ inputFiles :+ InputFile(file, config("annotation_bed_md5", freeVar = true))
file
}
}
@@ -28,8 +28,8 @@ trait AnnotationBed extends BiopetQScript { qscript: QScript =>
trait AnnotationRefFlat extends BiopetQScript { qscript: QScript =>
/** GTF reference file */
lazy val annotationRefFlat: File = {
- val file: File = config("annotation_refflat")
- inputFiles :+ InputFile(file, config("annotation_refflat_md5"))
+ val file: File = config("annotation_refflat", freeVar = true)
+ inputFiles :+ InputFile(file, config("annotation_refflat_md5", freeVar = true))
file
}
}
@@ -37,8 +37,8 @@ trait AnnotationRefFlat extends BiopetQScript { qscript: QScript =>
trait RibosomalRefFlat extends BiopetQScript { qscript: QScript =>
/** GTF reference file */
lazy val ribosomalRefFlat: File = {
- val file: File = config("ribosome_refflat")
- inputFiles :+ InputFile(file, config("ribosome_refflat_md5"))
+ val file: File = config("ribosome_refflat", freeVar = true)
+ inputFiles :+ InputFile(file, config("ribosome_refflat_md5", freeVar = true))
file
}
}
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
index 3803b5dce..43f2a4806 100644
--- 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
@@ -4,21 +4,8 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.QScript
/**
- * Created by pjvan_thof on 1/12/16.
- */
+ * Created by pjvan_thof on 1/12/16.
+ */
class BasesPerExon(val root: Configurable) extends QScript with Measurement {
- /** Init for pipeline */
- def init(): Unit = ???
-
- /** Pipeline itself */
- def biopetScript(): Unit = ???
-
- /** 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()
-
- /** Name of summary output file */
- def summaryFile: File = new File("BasesPerExon.summary.json")
+ def bamToCountFile(id: String, bamFile: File): (String, File) = ???
}
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
index a550a02c1..599fb670c 100644
--- 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
@@ -4,21 +4,9 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.QScript
/**
- * Created by pjvan_thof on 1/12/16.
- */
+ * Created by pjvan_thof on 1/12/16.
+ */
class BasesPerGene(val root: Configurable) extends QScript with Measurement {
- /** Init for pipeline */
- def init(): Unit = ???
-
- /** Pipeline itself */
- def biopetScript(): Unit = ???
-
- /** 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()
-
- /** Name of summary output file */
- def summaryFile: File = new File("BasesPerGene.summary.json")
+ //TODO: splitting on strand if strandspecific
+ def bamToCountFile(id: String, bamFile: File): (String, File) = ???
}
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/CufflinksBlind.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/CufflinksBlind.scala
index 3615540f2..f24e0ed80 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/CufflinksBlind.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/CufflinksBlind.scala
@@ -4,21 +4,8 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.QScript
/**
- * Created by pjvan_thof on 1/12/16.
- */
+ * Created by pjvan_thof on 1/12/16.
+ */
class CufflinksBlind(val root: Configurable) extends QScript with Measurement {
- /** Init for pipeline */
- def init(): Unit = ???
-
- /** Pipeline itself */
- def biopetScript(): Unit = ???
-
- /** 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()
-
- /** Name of summary output file */
- def summaryFile: File = new File("CufflinksBlind.summary.json")
+ def bamToCountFile(id: String, bamFile: File): (String, File) = ???
}
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/CufflinksGuided.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/CufflinksGuided.scala
index 900c707f6..a8b3e845a 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/CufflinksGuided.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/CufflinksGuided.scala
@@ -4,21 +4,8 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.QScript
/**
- * Created by pjvan_thof on 1/12/16.
- */
+ * Created by pjvan_thof on 1/12/16.
+ */
class CufflinksGuided(val root: Configurable) extends QScript with Measurement {
- /** Init for pipeline */
- def init(): Unit = ???
-
- /** Pipeline itself */
- def biopetScript(): Unit = ???
-
- /** 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()
-
- /** Name of summary output file */
- def summaryFile: File = new File("CufflinksGuided.summary.json")
+ def bamToCountFile(id: String, bamFile: File): (String, File) = ???
}
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/CufflinksStrict.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/CufflinksStrict.scala
index 0055d46bc..5fa3ce96f 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/CufflinksStrict.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/CufflinksStrict.scala
@@ -4,21 +4,8 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.QScript
/**
- * Created by pjvan_thof on 1/12/16.
- */
+ * Created by pjvan_thof on 1/12/16.
+ */
class CufflinksStrict(val root: Configurable) extends QScript with Measurement {
- /** Init for pipeline */
- def init(): Unit = ???
-
- /** Pipeline itself */
- def biopetScript(): Unit = ???
-
- /** 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()
-
- /** Name of summary output file */
- def summaryFile: File = new File("CufflinksStrict.summary.json")
+ def bamToCountFile(id: String, bamFile: File): (String, File) = ???
}
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 623dd039b..1d1fbb56e 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
@@ -4,21 +4,8 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.QScript
/**
- * Created by pjvan_thof on 1/12/16.
- */
+ * Created by pjvan_thof on 1/12/16.
+ */
class FragmentsPerExon(val root: Configurable) extends QScript with Measurement {
- /** Init for pipeline */
- def init(): Unit = ???
-
- /** Pipeline itself */
- def biopetScript(): Unit = ???
-
- /** 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()
-
- /** Name of summary output file */
- def summaryFile: File = new File("FragmentsPerExon.summary.json")
+ def bamToCountFile(id: String, bamFile: File): (String, File) = ???
}
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 c3c24e268..904fcde16 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
@@ -4,21 +4,8 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.QScript
/**
- * Created by pjvan_thof on 1/12/16.
- */
+ * Created by pjvan_thof on 1/12/16.
+ */
class FragmentsPerGene(val root: Configurable) extends QScript with Measurement {
- /** Init for pipeline */
- def init(): Unit = ???
-
- /** Pipeline itself */
- def biopetScript(): Unit = ???
-
- /** 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()
-
- /** Name of summary output file */
- def summaryFile: File = new File("FragmentsPerGene.summary.json")
+ def bamToCountFile(id: String, bamFile: File): (String, File) = ???
}
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 eb39c09c9..37249c593 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
@@ -5,13 +5,40 @@ import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import org.broadinstitute.gatk.queue.QScript
/**
- * Created by pjvan_thof on 1/12/16.
- */
-trait Measurement extends SummaryQScript with Reference { qscript : QScript =>
- private var bamFiles: Map[String, File] = Map()
+ * Created by pjvan_thof on 1/12/16.
+ */
+trait Measurement extends SummaryQScript with Reference { qscript: QScript =>
+ protected var bamFiles: Map[String, File] = Map()
def addBamfile(id: String, file: File): Unit = {
require(!bamFiles.contains(id), s"'$id' already exist")
bamFiles += id -> file
}
+
+ def name: String = this.getClass.getSimpleName.toLowerCase
+
+ lazy val countFiles: Map[String, File] = bamFiles.map { case (id, bamFile) => bamToCountFile(id, bamFile) }
+
+ /** Init for pipeline */
+ def init(): Unit = {
+ require(bamFiles.nonEmpty)
+ }
+
+ /** Pipeline itself */
+ def biopetScript(): Unit = {
+ //TODO: Merging
+
+ //TODO: Heatmap
+ }
+
+ def bamToCountFile(id: String, bamFile: File): (String, File)
+
+ /** Must return a map with used settings for this pipeline */
+ def summarySettings: Map[String, Any] = Map()
+
+ /** File to put in the summary for thie pipeline */
+ def summaryFiles: Map[String, File] = Map()
+
+ /** Name of summary output file */
+ def summaryFile: File = new File(s"$name.summary.json")
}
--
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