summary for vep

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

@@ -17,16 +17,19 @@ package nl.lumc.sasc.biopet.extensions
 
 import java.io.File
 
+import nl.lumc.sasc.biopet.core.summary.Summarizable
 import nl.lumc.sasc.biopet.utils.Logging
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import nl.lumc.sasc.biopet.core.{ Version, BiopetCommandLineFunction, Reference }
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
+import scala.io.Source
+
 /**
  * Extension for VariantEffectPredictor
  * Created by ahbbollen on 15-1-15.
  */
-class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFunction with Reference with Version {
+class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFunction with Reference with Version with Summarizable {
 
   executable = config("exe", submodule = "perl", default = "perl")
   var vepScript: String = config("vep_script")
@@ -48,7 +51,7 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
   var everything: Boolean = config("everything", default = false)
   var force: Boolean = config("force", default = false)
   var no_stats: Boolean = config("no_stats", default = false)
-  var stats_text: Boolean = config("stats_text", default = false)
+  var stats_text: Boolean = config("stats_text", default = true)
   var html: Boolean = config("html", default = false)
   var cache: Boolean = config("cache", default = false)
   var humdiv: Boolean = config("humdiv", default = false)
@@ -254,4 +257,48 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
     optional("--buffer_size", buffer_size) +
     optional("--failed", failed)
 
+  def summaryFiles: Map[String, File] = Map()
+
+  def summaryStats: Map[String, Any] = {
+    if (stats_text) {
+      val stats_file: File = new File(output.getAbsolutePath + "_summary.txt")
+      parseStatsFile(stats_file)
+    } else {
+      Map()
+    }
+  }
+
+  def parseStatsFile(file: File): Map[String, Any] = {
+    val contents = Source.fromFile(file).getLines().toList
+    val headers = getHeadersFromStatsFile(contents)
+    headers.foldLeft(Map[String, Any]())((acc, x) => getBlockFromStatsFile(contents, x))
+  }
+
+  def getBlockFromStatsFile(contents: List[String], header: String): Map[String, Any] = {
+    var inBlock = false
+    var theMap: Map[String, Any] = Map()
+    for (x <- contents) {
+      val stripped = x.stripPrefix("[").stripSuffix("]")
+      if (stripped == header) {
+        inBlock = true
+      }
+      if (stripped == "") {
+        inBlock = false
+      }
+
+      if (inBlock) {
+        val key = stripped.split('\t').head.replace(" ", "_")
+        val value = stripped.split('\t').last
+        theMap ++= Map(key -> value)
+
+      }
+    }
+    theMap
+  }
+
+  def getHeadersFromStatsFile(contents: List[String]): List[String] = {
+    // block headers are of format '[block]'
+    contents.filter(_.startsWith("[")).filter(_.endsWith("]")).map(_.stripPrefix("[")).map(_.stripSuffix("]"))
+  }
+
 }

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

@@ -89,10 +89,10 @@ object SeqStat extends ToolCommand {
 
     (qual_low_boundery < 59, qual_high_boundery > 74) match {
       case (false, true) => phredEncoding = Solexa
-        // TODO: check this later on
-        // complex case, we cannot tell wheter this is a sanger or solexa
-        // but since the qual_high_boundery exceeds any Sanger/Illumina1.8 quals, we can `assume` this is solexa
-        // New @ 2016/01/26: Illumina X ten samples can contain Phred=Q42 (qual_high_boundery==75/K)
+      // TODO: check this later on
+      // complex case, we cannot tell wheter this is a sanger or solexa
+      // but since the qual_high_boundery exceeds any Sanger/Illumina1.8 quals, we can `assume` this is solexa
+      // New @ 2016/01/26: Illumina X ten samples can contain Phred=Q42 (qual_high_boundery==75/K)
       case (true, true)  => phredEncoding = Solexa
       // this is definite a sanger sequence, the lower end is sanger only
       case (true, false) => phredEncoding = Sanger
@@ -181,7 +181,7 @@ object SeqStat extends ToolCommand {
         quals ++= mutable.ArrayBuffer.fill(baseStats(pos).qual.length - quals.length)(0)
       }
       if (nucs.length <= baseStats(pos).nucs.length) {
-        nucs ++= mutable.ArrayBuffer.fill( baseStats(pos).nucs.length - nucs.length )(0)
+        nucs ++= mutable.ArrayBuffer.fill(baseStats(pos).nucs.length - nucs.length)(0)
       }
       // count into the quals
       baseStats(pos).qual.zipWithIndex foreach { case (value, index) => quals(index) += value }

public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala

@@ -68,6 +68,7 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
     vep.output = new File(outputDir, inputVCF.getName.stripSuffix(".gz").stripSuffix(".vcf") + ".vep.vcf")
     vep.isIntermediate = true
     add(vep)
+    addSummarizable(vep, "variant_effect_predictor")
 
     val normalizer = new VepNormalizer(this)
     normalizer.inputVCF = vep.output