Added tool for merging otu maps

public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeOtuMaps.scala

+/**
+ * Biopet is built on top of GATK Queue for building bioinformatic
+ * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+ * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+ * should also be able to execute Biopet tools and pipelines.
+ *
+ * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+ *
+ * Contact us at: sasc@lumc.nl
+ *
+ * A dual licensing mode is applied. The source code within this project that are
+ * not part of GATK Queue is freely available for non-commercial use under an AGPL
+ * license; For commercial users or users who do not want to follow the AGPL
+ * license, please contact us to obtain a separate license.
+ */
+package nl.lumc.sasc.biopet.extensions.tools
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.ToolCommandFunction
+import nl.lumc.sasc.biopet.core.summary.Summarizable
+import nl.lumc.sasc.biopet.utils.ConfigUtils
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
+class MergeOtuMaps(val root: Configurable) extends ToolCommandFunction {
+  def toolObject = nl.lumc.sasc.biopet.tools.MergeOtuMaps
+
+  @Input(doc = "Input", shortName = "input", required = true)
+  var input: List[File] = Nil
+
+  @Output(doc = "Output", shortName = "output", required = true)
+  var output: File = _
+
+  override def defaultCoreMemory = 6.0
+
+  override def cmdLine = super.cmdLine + repeat("-I", input) + required("-o", output)
+
+}
+

public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MergeOtuMaps.scala

+package nl.lumc.sasc.biopet.tools
+
+import java.io.{ PrintWriter, File }
+
+import nl.lumc.sasc.biopet.utils.ToolCommand
+
+import scala.io.Source
+
+/**
+ * Created by pjvan_thof on 12/18/15.
+ */
+object MergeOtuMaps extends ToolCommand {
+  case class Args(inputFiles: List[File] = Nil, outputFile: File = null) extends AbstractArgs
+
+  class OptParser extends AbstractOptParser {
+    opt[File]('I', "input") minOccurs 2 required () unbounded () valueName "<file>" action { (x, c) =>
+      c.copy(inputFiles = x :: c.inputFiles)
+    }
+    opt[File]('o', "output") required () unbounded () maxOccurs 1 valueName "<file>" action { (x, c) =>
+      c.copy(outputFile = x)
+    }
+  }
+
+  /**
+   * @param args the command line arguments
+   */
+  def main(args: Array[String]): Unit = {
+    val argsParser = new OptParser
+    val commandArgs: Args = argsParser.parse(args, Args()) getOrElse sys.exit(1)
+
+    var map: Map[Long, String] = Map()
+
+    for (inputFile <- commandArgs.inputFiles) {
+      logger.info(s"Start reading $inputFile")
+      val reader = Source.fromFile(inputFile)
+      reader.getLines().foreach { line =>
+        val values = line.split("\t", 2)
+        val key = values.head.toLong
+        map += key -> (line.stripPrefix(s"$key") + map.getOrElse(key, ""))
+      }
+      reader.close()
+    }
+
+    logger.info(s"Start writing to ${commandArgs.outputFile}")
+    val writer = new PrintWriter(commandArgs.outputFile)
+    map.foreach { case (key, list) => writer.println(key + list) }
+    writer.close()
+  }
+}

public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala

 package nl.lumc.sasc.biopet.pipelines.gears
 
 import nl.lumc.sasc.biopet.core.{ PipelineCommand, MultiSampleQScript }
+import nl.lumc.sasc.biopet.extensions.tools.MergeOtuMaps
 import nl.lumc.sasc.biopet.extensions.{ Gzip, Zcat, Ln }
-import nl.lumc.sasc.biopet.extensions.qiime.{ MergeOtuMaps, MergeOtuTables }
+import nl.lumc.sasc.biopet.extensions.qiime.MergeOtuTables
 import nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.QScript
@@ -56,7 +57,7 @@ class Gears(val root: Configurable) extends QScript with MultiSampleQScript { qs
 
         val mergeMaps = new MergeOtuMaps(qscript)
         mergeMaps.input = closedOtuMaps
-        mergeMaps.outputFile = closedOtuMap
+        mergeMaps.output = closedOtuMap
         add(mergeMaps)
 
       } else {