From c294fbefe830b7e286743f8939bff9e5a7b63351 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 29 Jan 2016 11:02:15 +0100
Subject: [PATCH] Added meta exon counts to pipeline
---
.../lumc/sasc/biopet/extensions/tools/BaseCounter.scala | 8 +++++++-
.../biopet/pipelines/gentrap/measures/BaseCounts.scala | 4 ++++
2 files changed, 11 insertions(+), 1 deletion(-)
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BaseCounter.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BaseCounter.scala
index 05a3025ef..16348d31b 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BaseCounter.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BaseCounter.scala
@@ -71,6 +71,10 @@ class BaseCounter(val root: Configurable) extends ToolCommandFunction {
def mergeIntronCounts = new File(outputDir, s"$prefix.base.intron.merge.counts")
def mergeIntronSenseCounts = new File(outputDir, s"$prefix.base.intron.merge.sense.counts")
def mergeIntronAntiSenseCounts = new File(outputDir, s"$prefix.base.intron.merge.antisense.counts")
+ def nonStrandedMetaExonCounts = new File(outputDir, s"$prefix.base.metaexons.non_stranded.counts")
+ def strandedMetaExonCounts = new File(outputDir, s"$prefix.base.metaexons.stranded.counts")
+ def strandedSenseMetaExonCounts = new File(outputDir, s"$prefix.base.metaexons.stranded.sense.counts")
+ def strandedAntiSenseMetaExonCounts = new File(outputDir, s"$prefix.base.metaexons.stranded.antisense.counts")
override def beforeGraph(): Unit = {
super.beforeGraph()
@@ -83,7 +87,9 @@ class BaseCounter(val root: Configurable) extends ToolCommandFunction {
geneExonicCounts, geneExonicSenseCounts, geneExonicAntiSenseCounts,
geneIntronicCounts, geneIntronicSenseCounts, geneIntronicAntiSenseCounts,
mergeExonCounts, mergeExonSenseCounts, mergeExonAntiSenseCounts,
- mergeIntronCounts, mergeIntronSenseCounts, mergeIntronAntiSenseCounts)
+ mergeIntronCounts, mergeIntronSenseCounts, mergeIntronAntiSenseCounts,
+ nonStrandedMetaExonCounts,
+ strandedMetaExonCounts, strandedSenseMetaExonCounts, strandedAntiSenseMetaExonCounts)
}
override def cmdLine = super.cmdLine +
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
index 98d1aeed3..d54fc2b33 100644
--- 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
@@ -63,5 +63,9 @@ class BaseCounts(val root: Configurable) extends QScript with Measurement with A
addTableAndHeatmap(jobs.values.map(_.mergeIntronCounts).toList, "mergeIntronCounts")
addTableAndHeatmap(jobs.values.map(_.mergeIntronSenseCounts).toList, "mergeIntronSenseCounts")
addTableAndHeatmap(jobs.values.map(_.mergeIntronAntiSenseCounts).toList, "mergeIntronAntiSenseCounts")
+ addTableAndHeatmap(jobs.values.map(_.nonStrandedMetaExonCounts).toList, "nonStrandedMetaExonCounts")
+ addTableAndHeatmap(jobs.values.map(_.strandedMetaExonCounts).toList, "strandedMetaExonCounts")
+ addTableAndHeatmap(jobs.values.map(_.strandedSenseMetaExonCounts).toList, "strandedSenseMetaExonCounts")
+ addTableAndHeatmap(jobs.values.map(_.strandedAntiSenseMetaExonCounts).toList, "strandedAntiSenseMetaExonCounts")
}
}
--
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