From bf6c2be4a69032233c2046793f77c8903c153597 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 20 Oct 2015 23:25:45 +0200
Subject: [PATCH] More piping for target flagstat
---
.../pipelines/bammetrics/BamMetrics.scala | 20 ++++++-------------
.../bammetrics/scripts/CoverageStats.scala | 7 +++----
.../bedtools/BedtoolsCoverage.scala | 4 ++--
.../bedtools/BedtoolsIntersect.scala | 4 ++++
4 files changed, 15 insertions(+), 20 deletions(-)
diff --git a/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala b/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
index ed89542f2..3e6059b1c 100644
--- a/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
+++ b/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
@@ -151,29 +151,21 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
val targetDir = new File(outputDir, targetName)
val biStrict = BedtoolsIntersect(this, inputBam, intervals.bed,
- output = new File(targetDir, inputBam.getName.stripSuffix(".bam") + ".overlap.strict.bam"),
+ output = new File(targetDir, inputBam.getName.stripSuffix(".bam") + ".overlap.strict.sam"),
minOverlap = config("strict_intersect_overlap", default = 1.0))
- biStrict.isIntermediate = true
- add(biStrict)
- add(SamtoolsFlagstat(this, biStrict.output, targetDir))
val biopetFlagstatStrict = BiopetFlagstat(this, biStrict.output, targetDir)
- add(biopetFlagstatStrict)
addSummarizable(biopetFlagstatStrict, targetName + "_biopet_flagstat_strict")
+ add(new BiopetFifoPipe(this, List(biStrict, biopetFlagstatStrict)))
val biLoose = BedtoolsIntersect(this, inputBam, intervals.bed,
- output = new File(targetDir, inputBam.getName.stripSuffix(".bam") + ".overlap.loose.bam"),
+ output = new File(targetDir, inputBam.getName.stripSuffix(".bam") + ".overlap.loose.sam"),
minOverlap = config("loose_intersect_overlap", default = 0.01))
- biLoose.isIntermediate = true
- add(biLoose)
- add(SamtoolsFlagstat(this, biLoose.output, targetDir))
val biopetFlagstatLoose = BiopetFlagstat(this, biLoose.output, targetDir)
- add(biopetFlagstatLoose)
addSummarizable(biopetFlagstatLoose, targetName + "_biopet_flagstat_loose")
+ add(new BiopetFifoPipe(this, List(biLoose, biopetFlagstatLoose)))
- val coverageFile = new File(targetDir, inputBam.getName.stripSuffix(".bam") + ".coverage")
-
- val bedCov = BedtoolsCoverage(this, inputBam, intervals.bed, coverageFile, depth = true)
- val covStats = CoverageStats(this, coverageFile, targetDir)
+ val bedCov = BedtoolsCoverage(this, inputBam, intervals.bed, depth = true)
+ val covStats = CoverageStats(this, targetDir, inputBam.getName.stripSuffix(".bam") + ".coverage")
covStats.title = Some("Coverage for " + targetName)
covStats.subTitle = Some(".")
add(bedCov | covStats)
diff --git a/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/scripts/CoverageStats.scala b/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/scripts/CoverageStats.scala
index 4a4795cf9..a12aced89 100644
--- a/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/scripts/CoverageStats.scala
+++ b/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/scripts/CoverageStats.scala
@@ -55,11 +55,10 @@ class CoverageStats(val root: Configurable) extends PythonCommandLineFunction wi
}
object CoverageStats {
- def apply(root: Configurable, input: File, outputDir: File): CoverageStats = {
+ def apply(root: Configurable, outputDir: File, name: String): CoverageStats = {
val coverageStats = new CoverageStats(root)
- coverageStats.input = input
- coverageStats.output = new File(outputDir, input.getName + ".stats")
- coverageStats.plot = new File(outputDir, input.getName + ".stats.png")
+ coverageStats.output = new File(outputDir, name + ".stats")
+ coverageStats.plot = new File(outputDir, name + ".stats.png")
coverageStats
}
}
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala
index efb3c1abe..8b1476857 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala
@@ -61,12 +61,12 @@ class BedtoolsCoverage(val root: Configurable) extends Bedtools {
object BedtoolsCoverage {
/** Returns defaul bedtools coverage */
- def apply(root: Configurable, input: File, intersect: File, output: File,
+ def apply(root: Configurable, input: File, intersect: File, output: Option[File] = None,
depth: Boolean = true, sameStrand: Boolean = false, diffStrand: Boolean = false): BedtoolsCoverage = {
val bedtoolsCoverage = new BedtoolsCoverage(root)
bedtoolsCoverage.input = input
bedtoolsCoverage.intersectFile = intersect
- bedtoolsCoverage.output = output
+ output.foreach(bedtoolsCoverage.output = _)
bedtoolsCoverage.depth = depth
bedtoolsCoverage.sameStrand = sameStrand
bedtoolsCoverage.diffStrand = diffStrand
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala
index 75f179ad3..bbd110c88 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala
@@ -40,6 +40,8 @@ class BedtoolsIntersect(val root: Configurable) extends Bedtools {
var inputTag = "-a"
+ var ubam = false
+
override def beforeCmd() {
if (input.getName.endsWith(".bam")) inputTag = "-abam"
}
@@ -50,6 +52,7 @@ class BedtoolsIntersect(val root: Configurable) extends Bedtools {
required("-b", intersectFile) +
optional("-f", minOverlap) +
conditional(count, "-c") +
+ conditional(ubam, "-ubam") +
" > " + required(output)
}
@@ -61,6 +64,7 @@ object BedtoolsIntersect {
bedtoolsIntersect.input = input
bedtoolsIntersect.intersectFile = intersect
bedtoolsIntersect.output = output
+ if (output.getName.endsWith(".sam")) bedtoolsIntersect.ubam = true
bedtoolsIntersect.minOverlap = minOverlap
bedtoolsIntersect.count = count
bedtoolsIntersect
--
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