From 22064e83561421f12a7178c1e7f9dd57969033e3 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Sat, 22 Aug 2015 20:37:20 +0200
Subject: [PATCH] Add nested option to originals
---
.../nl/lumc/sasc/biopet/tools/RegionAfCount.scala | 10 +++-------
.../sasc/biopet/utils/intervals/BedRecord.scala | 14 +++++++++-----
2 files changed, 12 insertions(+), 12 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/RegionAfCount.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/RegionAfCount.scala
index ad29bd5f7..8ba1caabd 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/RegionAfCount.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/RegionAfCount.scala
@@ -40,8 +40,7 @@ object RegionAfCount extends ToolCommand {
case class Args(bedFile: File = null,
outputFile: File = null,
scatterpPlot: Option[File] = None,
- vcfFiles: List[File] = Nil,
- exonsOnly: Boolean = false) extends AbstractArgs
+ vcfFiles: List[File] = Nil) extends AbstractArgs
class OptParser extends AbstractOptParser {
opt[File]('b', "bedFile") required () maxOccurs 1 valueName "<file>" action { (x, c) =>
@@ -56,9 +55,6 @@ object RegionAfCount extends ToolCommand {
opt[File]('V', "vcfFile") unbounded () minOccurs 1 action { (x, c) =>
c.copy(vcfFiles = c.vcfFiles ::: x :: Nil)
}
- opt[Unit]("exonsOnly") unbounded () action { (x, c) =>
- c.copy(exonsOnly = true)
- }
}
def main(args: Array[String]): Unit = {
@@ -89,8 +85,8 @@ object RegionAfCount extends ToolCommand {
case a: util.ArrayList[_] => a.map(_.toString.toDouble).toArray
case s => Array(s.toString.toDouble)
}).sum
- region.originals
- .map(_.name.getOrElse("error"))
+ region.originals()
+ .map(x => x.name.getOrElse(s"${x.chr}:${x.start}-${x.end}"))
.distinct
.foreach(name => afCounts += name -> (afCounts.getOrElse(name, 0.0) + sum))
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecord.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecord.scala
index 58901c955..d396464ff 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecord.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecord.scala
@@ -18,7 +18,11 @@ case class BedRecord(chr: String,
protected[intervals] var _originals: List[BedRecord] = Nil
- def originals = _originals
+ def originals(nested: Boolean = false): List[BedRecord] = {
+ if (_originals.isEmpty) List(this)
+ else if (nested) _originals.flatMap(_.originals(true))
+ else _originals
+ }
lazy val exons = if (blockCount.isDefined && blockSizes.length > 0 && blockStarts.length > 0) {
Some(BedRecordList.fromList(for (i <- 0 to blockCount.get) yield {
@@ -62,14 +66,14 @@ object BedRecord {
values(2).toInt,
values.lift(3),
values.lift(4).map(_.toInt),
- values.lift(5).map(_ match {
+ values.lift(5).map {
case "-" => false
case "+" => true
- case _ => throw new IllegalStateException("Strand (column 6) must be '+' or '-'")
- }),
+ case _ => throw new IllegalStateException("Strand (column 6) must be '+' or '-'")
+ },
values.lift(6).map(_.toInt),
values.lift(7) map (_.toInt),
- values.lift(8).map(_.split(",", 3).map(_.toInt)).map(x => (x.lift(0).getOrElse(0), x.lift(1).getOrElse(0), x.lift(2).getOrElse(0))),
+ values.lift(8).map(_.split(",", 3).map(_.toInt)).map(x => (x.headOption.getOrElse(0), x.lift(1).getOrElse(0), x.lift(2).getOrElse(0))),
values.lift(9).map(_.toInt),
values.lift(10).map(_.split(",").map(_.toInt)).getOrElse(Array()),
values.lift(11).map(_.split(",").map(_.toInt)).getOrElse(Array())
--
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