Added SplitLibrariesFastq

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/SplitLibrariesFastq.scala

+package nl.lumc.sasc.biopet.extensions.qiime
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.{Version, BiopetCommandLineFunction}
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.Input
+
+/**
+  * Created by pjvan_thof on 12/10/15.
+  */
+class SplitLibrariesFastq(val root: Configurable) extends BiopetCommandLineFunction with Version {
+  executable = config("exe", default = "split_libraries_fastq.py")
+
+  def versionCommand = executable + " --version"
+  def versionRegex = """Version: (.*)""".r
+
+  @Input
+  var input: List[File] = Nil
+  var outputDir: File = _
+
+  var v: Option[String] = config("v")
+  var m: Option[String] = config("m")
+  var b: Option[String] = config("b")
+  var store_qual_scores: Boolean = config("store_qual_scores", default = false)
+  var sample_ids: List[String] = Nil
+  var store_demultiplexed_fastq: Boolean = config("store_demultiplexed_fastq", default = false)
+  var retain_unassigned_reads: Boolean = config("retain_unassigned_reads", default = false)
+  var r: Option[Int] = config("r")
+  var p: Option[Double] = config("p")
+  var n: Option[Int] = config("n")
+  var s: Option[Int] = config("s")
+  var rev_comp_barcode: Boolean = config("rev_comp_barcode", default = false)
+  var rev_comp_mapping_barcodes: Boolean = config("rev_comp_mapping_barcodes", default = false)
+  var rev_comp: Boolean = config("rev_comp", default = false)
+  var q: Option[Int] = config("q")
+  var last_bad_quality_char: Option[String] = config("last_bad_quality_char")
+  var barcode_type: Option[String] = config("barcode_type")
+  var max_barcode_errors: Option[Double] = config("max_barcode_errors")
+  var phred_offset: Option[String] = config("phred_offset")
+
+  def outputSeqs = new File(outputDir, "seqs.fna")
+
+  override def beforeGraph(): Unit = {
+    super.beforeGraph()
+    require(input.nonEmpty)
+    require(outputDir != null)
+    outputFiles :+= outputSeqs
+  }
+
+  def cmdLine = executable +
+    optional("-v", v) +
+    optional("-m", m) +
+    optional("-b", b) +
+    conditional(store_qual_scores, "--store_qual_scores") +
+    (sample_ids match {
+      case l: List[_] if l.nonEmpty => optional("--sample_ids", l.mkString(","))
+      case _ => ""
+    }) +
+    conditional(store_demultiplexed_fastq, "--store_demultiplexed_fastq") +
+    conditional(retain_unassigned_reads, "--retain_unassigned_reads") +
+    optional("-r", r) +
+    optional("-p", p) +
+    optional("-n", n) +
+    optional("-s", s) +
+    conditional(rev_comp_barcode, "--rev_comp_barcode") +
+    conditional(rev_comp_mapping_barcodes, "--rev_comp_mapping_barcodes") +
+    conditional(rev_comp, "--rev_comp") +
+    optional("-q", q) +
+    optional("--last_bad_quality_char", last_bad_quality_char) +
+    optional("--barcode_type", barcode_type) +
+    optional("--max_barcode_errors", max_barcode_errors) +
+    optional("--phred_offset", phred_offset) +
+    optional("-i", input) +
+    optional("-o", outputDir)
+}
\ No newline at end of file

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

 package nl.lumc.sasc.biopet.pipelines.gears
 
-import nl.lumc.sasc.biopet.core.BiopetQScript
-import nl.lumc.sasc.biopet.extensions.qiime.{ AssignTaxonomy, PickRepSet, PickOtus }
+import nl.lumc.sasc.biopet.core.{SampleLibraryTag, BiopetQScript}
+import nl.lumc.sasc.biopet.extensions.qiime.{SplitLibrariesFastq, AssignTaxonomy, PickRepSet, PickOtus}
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.QScript
 
 /**
  * Created by pjvan_thof on 12/4/15.
  */
-class GearsQiimeRtax(val root: Configurable) extends QScript with BiopetQScript {
+class GearsQiimeRtax(val root: Configurable) extends QScript with BiopetQScript with SampleLibraryTag {
 
-  var fastaR1: File = _
+  var fastqR1: File = _
 
-  var fastaR2: Option[File] = None
+  var fastqR2: Option[File] = None
 
   override def fixedValues = Map(
     "assigntaxonomy" -> Map(
@@ -25,25 +25,44 @@ class GearsQiimeRtax(val root: Configurable) extends QScript with BiopetQScript
       "otu_picking_method" -> "uclust_ref",
       "suppress_new_clusters" -> true,
       "enable_rev_strand_match" -> true
+    ),
+    "splitlibrariesfastq" -> Map(
+      "barcode_type" -> "not-barcoded"
     )
   )
 
   def init() = {
-    require(fastaR1 != null)
+    require(fastqR1 != null)
   }
 
   def biopetScript() = {
+
+    val slfR1 = new SplitLibrariesFastq(this)
+    slfR1.input :+= fastqR1
+    slfR1.outputDir = new File(outputDir, "split_libraries_fastq_R1")
+    sampleId.foreach(slfR1.sample_ids :+= _)
+    add(slfR1)
+
+    lazy val slfR2 = fastqR2.map { file =>
+      val j = new SplitLibrariesFastq(this)
+      j.input :+= file
+      j.outputDir = new File(outputDir, "split_libraries_fastq_R2")
+      sampleId.foreach(j.sample_ids :+= _)
+      add(j)
+      j
+    }
+
     val pickOtus = new PickOtus(this)
-    pickOtus.inputFasta = fastaR1
+    pickOtus.inputFasta = slfR1.outputSeqs
     pickOtus.outputDir = new File(outputDir, "pick_otus")
     add(pickOtus)
 
     val pickRepSet = new PickRepSet(this)
     val repSetOutputDir = new File(outputDir, "pick_rep_set")
     pickRepSet.inputFile = pickOtus.otusTxt
-    pickRepSet.fastaInput = Some(fastaR1)
-    pickRepSet.outputFasta = Some(new File(repSetOutputDir, fastaR1.getName))
-    pickRepSet.logFile = Some(new File(repSetOutputDir, fastaR1.getName
+    pickRepSet.fastaInput = Some(slfR1.outputSeqs)
+    pickRepSet.outputFasta = Some(new File(repSetOutputDir, slfR1.outputSeqs.getName))
+    pickRepSet.logFile = Some(new File(repSetOutputDir, slfR1.outputSeqs.getName
       .stripSuffix(".fasta").stripSuffix(".fa").stripSuffix(".fna") + ".log"))
     add(pickRepSet)
 
@@ -51,8 +70,8 @@ class GearsQiimeRtax(val root: Configurable) extends QScript with BiopetQScript
     assignTaxonomy.outputDir = new File(outputDir, "assign_taxonomy")
     assignTaxonomy.jobOutputFile = new File(assignTaxonomy.outputDir, ".assign_taxonomy.out")
     assignTaxonomy.inputFasta = pickRepSet.outputFasta.get
-    assignTaxonomy.read_1_seqs_fp = Some(fastaR1)
-    assignTaxonomy.read_2_seqs_fp = fastaR2
+    assignTaxonomy.read_1_seqs_fp = Some(slfR1.outputSeqs)
+    assignTaxonomy.read_2_seqs_fp = slfR2.map(_.outputSeqs)
     add(assignTaxonomy)
   }
 }

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

@@ -96,9 +96,6 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
     flexiprep.biopetScript()
     addAll(flexiprep.functions)
 
-    lazy val fastaR1 = fastqToFasta(flexiprep.fastqR1Qc, outputName + ".R1")
-    lazy val fastaR2 = flexiprep.fastqR2Qc.map(fastqToFasta(_, outputName + ".R2"))
-
     if (gearsUseKraken) {
       val kraken = new GearsKraken(this)
       kraken.outputDir = new File(outputDir, "kraken")
@@ -114,8 +111,8 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
     if (gearsUserQiimeRtax) {
       val qiimeRatx = new GearsQiimeRtax(this)
       qiimeRatx.outputDir = new File(outputDir, "qiime_rtax")
-      qiimeRatx.fastaR1 = fastaR1
-      qiimeRatx.fastaR2 = fastaR2
+      qiimeRatx.fastqR1 = flexiprep.fastqR1Qc
+      qiimeRatx.fastqR2 = flexiprep.fastqR2Qc
       qiimeRatx.init()
       qiimeRatx.biopetScript()
       addAll(qiimeRatx.functions)
@@ -135,18 +132,6 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
     (if (bamFile.isDefined) Map("input_bam" -> bamFile.get) else Map()) ++
     (if (fastqR1.isDefined) Map("input_R1" -> fastqR1.get) else Map()) ++
     outputFiles
-
-  def fastqToFasta(file: File, name: String): File = {
-    val seqtk = new SeqtkSeq(this) {
-      override def configName = "seqtkseq"
-      override def fixedValues = Map("A" -> true)
-    }
-    seqtk.input = file
-    seqtk.output = new File(outputDir, name + ".fasta")
-    seqtk.isIntermediate = true
-    add(seqtk)
-    seqtk.output
-  }
 }
 
 /** This object give a default main method to the pipelines */