From d7df6de4e38ed09a7b3cf747ea1356b47c7e43cd Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Sat, 22 Aug 2015 14:09:27 +0200
Subject: [PATCH] Code style fixes
---
.../extensions/rscript/ScatterPlot.scala | 2 +-
.../sasc/biopet/tools/RegionAfCount.scala | 22 ++++++------
.../nl/lumc/sasc/biopet/tools/SquishBed.scala | 36 +++++++++++++++++++
.../biopet/utils/intervals/BedRecord.scala | 10 +++---
4 files changed, 53 insertions(+), 17 deletions(-)
create mode 100644 public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SquishBed.scala
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/ScatterPlot.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/ScatterPlot.scala
index e03ce0b4b..f4cccdda1 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/ScatterPlot.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/ScatterPlot.scala
@@ -19,7 +19,7 @@ import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.extensions.RscriptCommandLineFunction
-import org.broadinstitute.gatk.utils.commandline.{Input, Output}
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
* Extension for en general line plot with R
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 7cf9e74b5..0435f9d6d 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
@@ -15,20 +15,20 @@
*/
package nl.lumc.sasc.biopet.tools
-import java.io.{PrintWriter, InputStream, File}
+import java.io.{ PrintWriter, InputStream, File }
import java.util
import htsjdk.samtools.util.Interval
-import htsjdk.samtools.{QueryInterval, SAMRecord, SamReader, SamReaderFactory}
+import htsjdk.samtools.{ QueryInterval, SAMRecord, SamReader, SamReaderFactory }
import htsjdk.tribble.AbstractFeatureReader._
-import htsjdk.tribble.{AbstractFeatureReader, TabixFeatureReader}
-import htsjdk.tribble.bed.{BEDFeature, SimpleBEDFeature, BEDCodec, FullBEDFeature}
-import htsjdk.variant.variantcontext.writer.{AsyncVariantContextWriter, VariantContextWriterBuilder}
-import htsjdk.variant.variantcontext.{VariantContext, VariantContextBuilder}
-import htsjdk.variant.vcf.{VCFFileReader, VCFHeaderLineCount, VCFHeaderLineType, VCFInfoHeaderLine}
+import htsjdk.tribble.{ AbstractFeatureReader, TabixFeatureReader }
+import htsjdk.tribble.bed.{ BEDFeature, SimpleBEDFeature, BEDCodec, FullBEDFeature }
+import htsjdk.variant.variantcontext.writer.{ AsyncVariantContextWriter, VariantContextWriterBuilder }
+import htsjdk.variant.variantcontext.{ VariantContext, VariantContextBuilder }
+import htsjdk.variant.vcf.{ VCFFileReader, VCFHeaderLineCount, VCFHeaderLineType, VCFInfoHeaderLine }
import nl.lumc.sasc.biopet.core.ToolCommand
import nl.lumc.sasc.biopet.extensions.rscript.ScatterPlot
-import nl.lumc.sasc.biopet.utils.intervals.{BedRecord, BedRecordList}
+import nl.lumc.sasc.biopet.utils.intervals.{ BedRecord, BedRecordList }
import scala.collection.JavaConversions._
import scala.collection.JavaConverters._
@@ -54,10 +54,10 @@ object RegionAfCount extends ToolCommand {
c.copy(scatterpPlot = Some(x))
}
opt[File]('V', "vcfFile") unbounded () minOccurs 1 action { (x, c) =>
- c.copy(vcfFiles = c.vcfFiles ::: x :: Nil )
+ c.copy(vcfFiles = c.vcfFiles ::: x :: Nil)
}
opt[Unit]("exonsOnly") unbounded () action { (x, c) =>
- c.copy(exonsOnly = true )
+ c.copy(exonsOnly = true)
}
}
@@ -87,7 +87,7 @@ object RegionAfCount extends ToolCommand {
for (variant <- it) {
val sum = (variant.getAttribute("AF", 0) match {
case a: util.ArrayList[_] => a.map(_.toString.toDouble).toArray
- case s => Array(s.toString.toDouble)
+ case s => Array(s.toString.toDouble)
}).sum
bedRecords
.overlapWith(BedRecord(variant.getContig, variant.getStart, variant.getEnd))
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SquishBed.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SquishBed.scala
new file mode 100644
index 000000000..41ac62d31
--- /dev/null
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SquishBed.scala
@@ -0,0 +1,36 @@
+package nl.lumc.sasc.biopet.tools
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.ToolCommand
+import nl.lumc.sasc.biopet.utils.intervals.BedRecordList
+
+/**
+ * Created by pjvanthof on 22/08/15.
+ */
+object SquishBed extends ToolCommand {
+
+ case class Args(input: File = null, output: File = null) extends AbstractArgs
+
+ class OptParser extends AbstractOptParser {
+ opt[File]('I', "input") required () valueName "<file>" action { (x, c) =>
+ c.copy(input = x)
+ }
+ opt[File]('o', "output") required () unbounded () valueName "<file>" action { (x, c) =>
+ c.copy(output = x)
+ }
+ }
+
+ /**
+ * @param args the command line arguments
+ */
+ def main(args: Array[String]): Unit = {
+ val argsParser = new OptParser
+ val cmdArgs: Args = argsParser.parse(args, Args()) getOrElse sys.exit(1)
+
+ if (!cmdArgs.input.exists) throw new IllegalStateException("Input file not found, file: " + cmdArgs.input)
+
+ val records = BedRecordList.fromFile(cmdArgs.input).squishBed()
+
+ }
+}
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 55f5907cc..58901c955 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
@@ -24,7 +24,7 @@ case class BedRecord(chr: String,
Some(BedRecordList.fromList(for (i <- 0 to blockCount.get) yield {
val exonNumber = strand match {
case Some(false) => blockCount.get - i
- case _ => i + 1
+ case _ => i + 1
}
val record = BedRecord(chr, start + blockStarts(i), start + blockStarts(i) + blockSizes(i),
name.map(_ + s"_exon-$exonNumber"))
@@ -37,7 +37,7 @@ case class BedRecord(chr: String,
Some(BedRecordList.fromList(for (i <- 0 to (blockCount.get - 1)) yield {
val intronNumber = strand match {
case Some(false) => blockCount.get - i
- case _ => i + 1
+ case _ => i + 1
}
val record = BedRecord(chr, start + start + blockStarts(i) + blockSizes(i) + 1, start + blockStarts(i + 1) - 1,
name.map(_ + s"_intron-$intronNumber"))
@@ -65,11 +65,11 @@ object BedRecord {
values.lift(5).map(_ match {
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(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(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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