write xcnv to bed tool

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/DepthOfCoverage.scala

@@ -20,42 +20,42 @@ class DepthOfCoverage(val root: Configurable) extends CommandLineGATK {
 
   @Output
   lazy val summaryFile: File = {
-    new File(out + "_summary")
+    new File(out + ".sample_summary")
   }
 
   @Output
   lazy val statisticsFile: File = {
-    new File(out + "_statistics")
+    new File(out + ".sample_statistics")
   }
 
   @Output
   lazy val intervalSummaryFile: File = {
-    new File(out + "_interval_summary")
+    new File(out + ".sample_interval_summary")
   }
 
   @Output
   lazy val intervalStatisticsFile: File = {
-    new File(out + "_interval_statistics")
+    new File(out + ".sample_interval_statistics")
   }
 
   @Output
   lazy val geneSummaryFile: File = {
-    new File(out + "_gene_summary")
+    new File(out + ".sample_gene_summary")
   }
 
   @Output
   lazy val geneStatisticsFile: File = {
-    new File(out + "_gene_statistics")
+    new File(out + ".sample_gene_statistics")
   }
 
   @Output
   lazy val cumulativeCoverageCountsFile: File = {
-    new File(out + "_cumulative_coverage_counts")
+    new File(out + ".sample_cumulative_coverage_counts")
   }
 
   @Output
   lazy val cumulativeCoverageProportionsFile: File = {
-    new File(out + "_cumulative_coverage_proportions")
+    new File(out + ".sample_cumulative_coverage_proportions")
   }
 
   @Argument(required = false)

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/XcnvToBed.scala

+package nl.lumc.sasc.biopet.tools
+
+import java.io.{BufferedWriter, File, FileWriter}
+
+import nl.lumc.sasc.biopet.tools.VepNormalizer.Args
+import nl.lumc.sasc.biopet.utils.ToolCommand
+
+import scala.io.Source
+
+/**
+  * Created by Sander Bollen on 24-11-16.
+  */
+object XcnvToBed extends ToolCommand {
+
+  def main(args: Array[String]): Unit = {
+    val commandArgs: Args = new OptParser()
+      .parse(args, Args())
+      .getOrElse(throw new IllegalArgumentException)
+
+
+    val writer = new BufferedWriter(new FileWriter(commandArgs.outputBed))
+    Source.fromFile(commandArgs.inputXcnv).
+      getLines().
+      filter(!_.startsWith("SAMPLE")).
+      map(x => x.split("\t")).
+      map(x => XcnvBedLine(x(0), x(1), x(2))).
+      filter(_.sample == commandArgs.sample).
+      foreach(x => writer.write(x.toString))
+  }
+
+  case class XcnvBedLine(sample: String, cnvType: String, location: String) {
+    override def toString: String = {
+      val cnv = if (cnvType == "DEL") {
+        -1
+      } else if (cnvType == "DUP") {
+        1
+      } else 0
+
+      val locs = location.split(":")
+      val chr = locs(0)
+      val start = locs(1).split("-")(0)
+      val stop = locs(1).split("-")(1)
+      s"$chr\t$start\t$stop\t$cnv"
+    }
+  }
+
+  case class Args(inputXcnv: File = null, outputBed: File = null , sample: String = null) extends AbstractArgs
+
+  class OptParser extends AbstractOptParser {
+    head("Convert a sample track within an XHMM XCNV file to a BED track. Fourt column indicates deletion (-1), normal (0) or duplication (1) of region")
+
+    opt[File]('I', "Input") required () valueName "<xcnv>" action { (x, c) =>
+      c.copy(inputXcnv = x)
+    } validate {
+      x => if (x.exists) success else failure("Input XCNV not found")
+    } text {
+      "Input XCNV file"
+    }
+    opt[File]('O', "Output") required() valueName "<bed>" action { (x,c) =>
+      c.copy(outputBed = x)
+    } text {
+      "Output BED file"
+    }
+    opt[String]('S', "Sample") required() action { (x,c) =>
+      c.copy(sample = x)
+    } text {
+      "The sample which to select"
+    }
+  }
+
+}