From 29ddfee68df64c2b4459fa74f4f90aa2bf72a7ad Mon Sep 17 00:00:00 2001
From: Sander Bollen <a.h.b.bollen@lumc.nl>
Date: Tue, 5 Jan 2016 12:10:45 +0100
Subject: [PATCH] merge bed file to prevent massive files
---
.../extensions/bedtools/BedtoolsMerge.scala | 28 +++++++++++++++++++
.../sasc/biopet/pipelines/toucan/Toucan.scala | 21 ++++++++++----
2 files changed, 44 insertions(+), 5 deletions(-)
create mode 100644 public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsMerge.scala
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsMerge.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsMerge.scala
new file mode 100644
index 000000000..c0f2e3640
--- /dev/null
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsMerge.scala
@@ -0,0 +1,28 @@
+package nl.lumc.sasc.biopet.extensions.bedtools
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Argument, Output, Input }
+
+/**
+ * Created by ahbbollen on 5-1-16.
+ */
+class BedtoolsMerge(val root: Configurable) extends Bedtools {
+
+ @Input(doc = "Input bed file")
+ var input: File = _
+
+ @Argument(doc = "Distance")
+ var dist: Int = 1 //default of tool is 1
+
+ @Output(doc = "Output bed file")
+ var output: File = _
+
+ def cmdLine = {
+ required(executable) + required("merge") +
+ required("-i", input) + optional("-d", dist) +
+ " > " + required(output)
+ }
+
+}
diff --git a/public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala b/public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
index 974df31da..620192846 100644
--- a/public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
+++ b/public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.pipelines.toucan
import java.io.{ File, PrintWriter }
import nl.lumc.sasc.biopet.extensions.bcftools.BcftoolsView
-import nl.lumc.sasc.biopet.extensions.bedtools.BedtoolsIntersect
+import nl.lumc.sasc.biopet.extensions.bedtools.{ BedtoolsMerge, BedtoolsIntersect }
import nl.lumc.sasc.biopet.extensions.manwe.{ ManweSamplesImport, ManweAnnotateVcf, ManweDataSourcesAnnotate }
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
@@ -131,9 +131,15 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
bedTrack.sample = Some(sampleID)
add(bedTrack)
+ val mergedBed = new BedtoolsMerge(this)
+ mergedBed.input = bedTrack.outputBed
+ mergedBed.dist = 5
+ mergedBed.output = swapExt(outputDir, bedTrack.outputBed, ".bed", ".merged.bed")
+ add(mergedBed)
+
val bgzippedBed = new Bgzip(this)
- bgzippedBed.input = List(bedTrack.outputBed)
- bgzippedBed.output = swapExt(outputDir, bedTrack.outputBed, ".bed", ".bed.gz")
+ bgzippedBed.input = List(mergedBed.output)
+ bgzippedBed.output = swapExt(outputDir, mergedBed.output, ".bed", ".bed.gz")
add(bgzippedBed)
val singleVcf = new BcftoolsView(this)
@@ -147,11 +153,16 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
val intersected = new BedtoolsIntersect(this)
intersected.input = singleVcf.output
intersected.intersectFile = bgzippedBed.output
- intersected.output = swapExt(outputDir, singleVcf.output, ".vcf.gz", ".intersected.vcf.gz")
+ intersected.output = swapExt(outputDir, singleVcf.output, ".vcf.gz", ".intersected.vcf")
add(intersected)
+ val bgzippedIntersect = new Bgzip(this)
+ bgzippedIntersect.input = List(intersected.output)
+ bgzippedIntersect.output = swapExt(outputDir, intersected.output, ".vcf", ".vcf.gz")
+ add(bgzippedIntersect)
+
val imported = new ManweSamplesImport(this)
- imported.vcfs = List(intersected.output)
+ imported.vcfs = List(bgzippedIntersect.output)
imported.beds = List(bgzippedBed.output)
imported.name = Some(sampleID)
imported.public = isPublic
--
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