diff --git a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVcfSampleCompare.scala b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVcfSampleCompare.scala
deleted file mode 100644
index c3f5add4b52092e607e1c4975745e7f58793dd08..0000000000000000000000000000000000000000
--- a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVcfSampleCompare.scala
+++ /dev/null
@@ -1,87 +0,0 @@
-/**
- * Due to the license issue with GATK, this part of Biopet can only be used inside the
- * LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
- * on how to use this protected part of biopet or contact us at sasc@lumc.nl
- */
-package nl.lumc.sasc.biopet.pipelines.gatk
-
-import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
-import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
-import nl.lumc.sasc.biopet.extensions.gatk.SelectVariants
-import nl.lumc.sasc.biopet.extensions.gatk.VariantEval
-import org.broadinstitute.gatk.queue.QScript
-import org.broadinstitute.gatk.utils.commandline.{ Input, Argument }
-
-class GatkVcfSampleCompare(val root: Configurable) extends QScript with BiopetQScript {
- def this() = this(null)
-
- @Input(doc = "Sample vcf file(s)", shortName = "V")
- var vcfFiles: List[File] = _
-
- @Argument(doc = "Reference", shortName = "R", required = false)
- var reference: File = config("reference")
-
- @Argument(doc = "Target bed", shortName = "targetBed", required = false)
- var targetBed: List[File] = Nil
-
- @Argument(doc = "Samples", shortName = "sample", required = false)
- var samples: List[String] = Nil
-
- var vcfFile: File = _
- var sampleVcfs: Map[String, File] = Map()
- def generalSampleDir = outputDir + "samples/"
-
- def init() {
- if (config.contains("target_bed"))
- for (bed <- config("target_bed").asList)
- targetBed :+= bed.toString
- if (outputDir == null) throw new IllegalStateException("Missing Output directory on gatk module")
- else if (!outputDir.endsWith("/")) outputDir += "/"
- }
-
- def biopetScript() {
- vcfFile = if (vcfFiles.size > 1) {
- val combineVariants = CombineVariants(this, vcfFiles, outputDir + "merge.vcf")
- add(combineVariants)
- combineVariants.out
- } else vcfFiles.head
-
- for (sample <- samples) {
- sampleVcfs += (sample -> new File(generalSampleDir + sample + File.separator + sample + ".vcf"))
- val selectVariants = SelectVariants(this, vcfFile, sampleVcfs(sample))
- selectVariants.sample_name = Seq(sample)
- selectVariants.excludeNonVariants = true
- add(selectVariants)
- }
-
- val sampleCompareMetrics = new SampleCompareMetrics(this)
- sampleCompareMetrics.samples = samples
- sampleCompareMetrics.sampleDir = generalSampleDir
- sampleCompareMetrics.snpRelFile = outputDir + "compare.snp.rel.tsv"
- sampleCompareMetrics.snpAbsFile = outputDir + "compare.snp.abs.tsv"
- sampleCompareMetrics.indelRelFile = outputDir + "compare.indel.rel.tsv"
- sampleCompareMetrics.indelAbsFile = outputDir + "compare.indel.abs.tsv"
- sampleCompareMetrics.totalFile = outputDir + "total.tsv"
-
- for ((sample, sampleVcf) <- sampleVcfs) {
- val sampleDir = generalSampleDir + sample + File.separator
- for ((compareSample, compareSampleVcf) <- sampleVcfs) {
- val variantEval = VariantEval(this,
- sampleVcf,
- compareSampleVcf,
- new File(sampleDir + sample + "-" + compareSample + ".eval.txt"),
- Seq("VariantType", "CompRod"),
- Seq("CompOverlap")
- )
- if (targetBed != null) variantEval.L = targetBed
- add(variantEval)
- sampleCompareMetrics.deps ::= variantEval.out
- }
- }
- add(sampleCompareMetrics)
- }
-}
-
-object GatkVcfSampleCompare extends PipelineCommand
diff --git a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/SampleCompareMetrics.scala b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/SampleCompareMetrics.scala
deleted file mode 100644
index 861455fe4d886219813409023d022ea096f413c9..0000000000000000000000000000000000000000
--- a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/SampleCompareMetrics.scala
+++ /dev/null
@@ -1,153 +0,0 @@
-/**
- * Due to the license issue with GATK, this part of Biopet can only be used inside the
- * LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
- * on how to use this protected part of biopet or contact us at sasc@lumc.nl
- */
-package nl.lumc.sasc.biopet.pipelines.gatk
-
-import java.io.File
-import java.io.PrintWriter
-import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
-import nl.lumc.sasc.biopet.core.config.Configurable
-import org.broadinstitute.gatk.utils.R.RScriptExecutor
-import org.broadinstitute.gatk.utils.commandline.{ Output, Argument }
-import scala.io.Source
-import org.broadinstitute.gatk.utils.R.{ RScriptLibrary, RScriptExecutor }
-import org.broadinstitute.gatk.utils.io.Resource
-import scala.collection.mutable.Map
-import scala.math._
-
-class SampleCompareMetrics(val root: Configurable) extends BiopetJavaCommandLineFunction {
- javaMainClass = getClass.getName
-
- @Argument(doc = "Sample Dir", shortName = "sampleDir", required = true)
- var sampleDir: String = _
-
- @Argument(doc = "Samples", shortName = "sample", required = true)
- var samples: List[String] = Nil
-
- @Argument(doc = "File sufix", shortName = "sufix", required = false)
- var fileSufix: String = _
-
- @Output(doc = "snpRelFile", shortName = "snpRelFile", required = true)
- var snpRelFile: File = _
-
- @Output(doc = "snpAbsFile", shortName = "snpAbsFile", required = true)
- var snpAbsFile: File = _
-
- @Output(doc = "indelRelFile", shortName = "indelRelFile", required = true)
- var indelRelFile: File = _
-
- @Output(doc = "indelAbsFile", shortName = "indelAbsFile", required = true)
- var indelAbsFile: File = _
-
- @Output(doc = "totalFile", shortName = "totalFile", required = true)
- var totalFile: File = _
-
- override val defaultVmem = "8G"
- memoryLimit = Option(4.0)
-
- override def commandLine = super.commandLine +
- required("-sampleDir", sampleDir) +
- repeat("-sample", samples) +
- optional("-fileSufix", fileSufix) +
- required("-snpRelFile", snpRelFile) +
- required("-snpAbsFile", snpAbsFile) +
- required("-indelRelFile", indelRelFile) +
- required("-indelAbsFile", indelAbsFile) +
- required("-totalFile", totalFile)
-}
-
-object SampleCompareMetrics {
- var sampleDir: String = _
- var samples: List[String] = Nil
- var fileSufix: String = ".eval.txt"
- var snpRelFile: File = _
- var snpAbsFile: File = _
- var indelRelFile: File = _
- var indelAbsFile: File = _
- var totalFile: File = _
- /**
- * @param args the command line arguments
- */
- def main(args: Array[String]): Unit = {
-
- for (t <- 0 until args.size) {
- args(t) match {
- case "-sample" => samples +:= args(t + 1)
- case "-sampleDir" => sampleDir = args(t + 1)
- case "-fileSufix" => fileSufix = args(t + 1)
- case "-snpRelFile" => snpRelFile = new File(args(t + 1))
- case "-snpAbsFile" => snpAbsFile = new File(args(t + 1))
- case "-indelRelFile" => indelRelFile = new File(args(t + 1))
- case "-indelAbsFile" => indelAbsFile = new File(args(t + 1))
- case "-totalFile" => totalFile = new File(args(t + 1))
- case _ =>
- }
- }
- if (sampleDir == null) throw new IllegalStateException("No sampleDir, use -sampleDir")
- else if (!sampleDir.endsWith("/")) sampleDir += "/"
-
- val regex = """\W+""".r
- val snpsOverlap: Map[(String, String), Int] = Map()
- val indelsOverlap: Map[(String, String), Int] = Map()
- val snpsTotal: Map[String, Int] = Map()
- val indelsTotal: Map[String, Int] = Map()
- for (sample1 <- samples; sample2 <- samples) {
- val reader = Source.fromFile(new File(sampleDir + sample1 + "/" + sample1 + "-" + sample2 + fileSufix))
- for (line <- reader.getLines) {
- regex.split(line) match {
- case Array(_, _, _, varType, all, novel, overlap, rate, _*) => {
- varType match {
- case "SNP" => {
- snpsOverlap += (sample1, sample2) -> overlap.toInt
- snpsTotal += sample1 -> all.toInt
- }
- case "INDEL" => {
- indelsOverlap += (sample1, sample2) -> overlap.toInt
- indelsTotal += sample1 -> all.toInt
- }
- case _ =>
- }
- }
- case _ =>
- }
- }
- reader.close()
- }
-
- val snpRelWritter = new PrintWriter(snpRelFile)
- val snpAbsWritter = new PrintWriter(snpAbsFile)
- val indelRelWritter = new PrintWriter(indelRelFile)
- val indelAbsWritter = new PrintWriter(indelAbsFile)
-
- val allWritters = List(snpRelWritter, snpAbsWritter, indelRelWritter, indelAbsWritter)
- for (writter <- allWritters) writter.println(samples.mkString("\t", "\t", ""))
- for (sample1 <- samples) {
- for (writter <- allWritters) writter.print(sample1)
- for (sample2 <- samples) {
- snpRelWritter.print("\t" + (round((snpsOverlap(sample1, sample2).toDouble / snpsTotal(sample1) * 10000.0)) / 10000.0))
- snpAbsWritter.print("\t" + snpsOverlap(sample1, sample2))
- indelRelWritter.print("\t" + (round((indelsOverlap(sample1, sample2).toDouble / indelsTotal(sample1) * 10000.0)) / 10000.0))
- indelAbsWritter.print("\t" + indelsOverlap(sample1, sample2))
- }
- for (writter <- allWritters) writter.println()
- }
- for (writter <- allWritters) writter.close()
-
- val totalWritter = new PrintWriter(totalFile)
- totalWritter.println("Sample\tSNPs\tIndels")
- for (sample <- samples)
- totalWritter.println(sample + "\t" + snpsTotal(sample) + "\t" + indelsTotal(sample))
- totalWritter.close()
-
- def plot(file: File) {
- val executor = new RScriptExecutor
- executor.addScript(new Resource("plotHeatmap.R", getClass))
- executor.addArgs(file, file.getAbsolutePath.stripSuffix(".tsv") + ".png", file.getAbsolutePath.stripSuffix(".tsv") + ".clustering.png")
- executor.exec()
- }
- plot(snpRelFile)
- plot(indelRelFile)
- }
-}
\ No newline at end of file
diff --git a/protected/biopet-protected-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutableProtected.scala b/protected/biopet-protected-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutableProtected.scala
index 9457fd36cfab986c5fdc9d5cbc29836ced4e0962..902e292fca017947affb287249ccff764e943100 100644
--- a/protected/biopet-protected-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutableProtected.scala
+++ b/protected/biopet-protected-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutableProtected.scala
@@ -12,7 +12,6 @@ object BiopetExecutableProtected extends BiopetExecutable {
nl.lumc.sasc.biopet.pipelines.gatk.GatkVariantcalling,
nl.lumc.sasc.biopet.pipelines.gatk.GatkPipeline,
nl.lumc.sasc.biopet.pipelines.gatk.GatkVariantRecalibration,
- nl.lumc.sasc.biopet.pipelines.gatk.GatkVcfSampleCompare,
nl.lumc.sasc.biopet.pipelines.basty.Basty)
def tools = BiopetExecutablePublic.tools
diff --git a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/pipelines/gatk/plotHeatmap.R b/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/pipelines/gatk/plotHeatmap.R
deleted file mode 100644
index 4158db708d58c8cc19b535dcfe871c626fa51ad6..0000000000000000000000000000000000000000
--- a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/pipelines/gatk/plotHeatmap.R
+++ /dev/null
@@ -1,24 +0,0 @@
-library('gplots')
-
-args <- commandArgs(TRUE)
-inputArg <- args[1]
-outputArg <- args[2]
-outputArgClustering <- args[3]
-
-col <- heat.colors(250)
-col[250] <- "#00FF00"
-
-heat<-read.table(inputArg, header = 1, sep= '\t')
-rownames(heat) <- heat[,1]
-heat<- heat[,-1]
-
-heat<- as.matrix(heat)
-
-png(file = outputArg, width = 1000, height = 1000)
-heatmap.2(heat, trace = 'none', col = col, Colv=NA, Rowv=NA, dendrogram="none")
-dev.off()
-
-
-png(file = outputArgClustering, width = 1000, height = 1000)
-heatmap.2(heat, trace = 'none', col = col, Colv="Rowv", dendrogram="row")
-dev.off()