Refactor seqstat and add (few) tests.. wip

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

@@ -37,6 +37,20 @@ object Seqstat extends ToolCommand {
   var phred_encoding: String = "sanger"
   var phred_correction: Int = 33
 
+  val reportValues = List(1, 10, 20, 30, 40, 50, 60)
+
+  // the base quality for each position on the reads
+  var quals: mutable.ArrayBuffer[Long] = mutable.ArrayBuffer()
+  var nucs: mutable.ArrayBuffer[Long] = mutable.ArrayBuffer()
+
+  // generate the baseHistogram and readHistogram
+  var baseHistogram: mutable.ArrayBuffer[Long] = mutable.ArrayBuffer()
+  var readHistogram: mutable.ArrayBuffer[Long] = mutable.ArrayBuffer()
+
+  var nucleotideHistoMap: mutable.Map[Char, Long] = mutable.Map()
+  var baseQualHistoMap: mutable.Map[Int, Long] = mutable.Map(0 -> 0)
+  var readQualHistoMap: mutable.Map[Int, Long] = mutable.Map(0 -> 0)
+
   case class Args(fastq: File = new File("")) extends AbstractArgs
 
   class OptParser extends AbstractOptParser {
@@ -125,30 +139,16 @@ object Seqstat extends ToolCommand {
     readQuals(avgQual) += 1
   }
 
-  def main(args: Array[String]): Unit = {
-
-    val commandArgs: Args = parseArgs(args)
-
-    logger.info("Start")
-    val reader = new FastqReader(commandArgs.fastq)
-    for (read <- reader.iterator.asScala) {
+  def seqStat(fqreader: FastqReader): (Long) = {
+    var numReads: Long = 0
+    for (read <- fqreader.iterator.asScala) {
       procesRead(read)
+      numReads += 1
     }
+    numReads
+  }
 
-    val reportValues = List(1, 10, 20, 30, 40, 50, 60)
-
-    // the base quality for each position on the reads
-    var quals: mutable.ArrayBuffer[Long] = mutable.ArrayBuffer()
-    var nucs: mutable.ArrayBuffer[Long] = mutable.ArrayBuffer()
-
-    // generate the baseHistogram and readHistogram
-    var baseHistogram: mutable.ArrayBuffer[Long] = mutable.ArrayBuffer()
-    var readHistogram: mutable.ArrayBuffer[Long] = mutable.ArrayBuffer()
-
-    var nucleotideHistoMap: mutable.Map[Char, Long] = mutable.Map()
-    var baseQualHistoMap: mutable.Map[Int, Long] = mutable.Map(0 -> 0)
-    var readQualHistoMap: mutable.Map[Int, Long] = mutable.Map(0 -> 0)
-
+  def summarize(): Unit = {
     // for every position to the max length of any read
     for (pos <- 0 until baseStats.length) {
       // list all qualities at this particular position `pos`
@@ -163,9 +163,7 @@ object Seqstat extends ToolCommand {
       baseStats(pos).qual.zipWithIndex foreach { case (value, index) => quals(index) += value }
       // count N into nucs
       baseStats(pos).nuc.zipWithIndex foreach { case (value, index) => nucs(index) += value }
-
     }
-
     detectPhredEncoding(quals)
 
     for (pos <- 0 until nucs.length) {
@@ -209,6 +207,18 @@ object Seqstat extends ToolCommand {
       readQualHistoMap += (pos -> readHistogram(pos))
     }
 
+  }
+
+  def main(args: Array[String]): Unit = {
+
+    val commandArgs: Args = parseArgs(args)
+
+    logger.info("Start")
+
+    val reader = new FastqReader(commandArgs.fastq)
+    seqStat(reader)
+    summarize()
+
     logger.debug(nucs)
     //    logger.debug(baseStats)
     logger.info("Done")

public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/SeqstatTest.scala

+/**
+ * Copyright (c) 2015 Leiden University Medical Center - Sequencing Analysis Support Core <sasc@lumc.nl>
+ * @author Wai Yi Leung <w.y.leung@lumc.nl>
+ */
+package nl.lumc.sasc.biopet.tools
+
+import java.io.File
+import java.nio.file.Paths
+
+import htsjdk.samtools.fastq.{ AsyncFastqWriter, FastqReader, FastqRecord }
+import nl.lumc.sasc.biopet.tools.FastqSync._
+import org.mockito.Mockito.{ inOrder => inOrd, when }
+import org.scalatest.Matchers
+import org.scalatest.mock.MockitoSugar
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.{ DataProvider, Test }
+
+import scala.collection.JavaConverters._
+
+class SeqstatTest extends TestNGSuite with MockitoSugar with Matchers {
+
+  import nl.lumc.sasc.biopet.tools.Seqstat._
+
+  private def resourceFile(p: String): File =
+    new File(resourcePath(p))
+
+  private def resourcePath(p: String): String =
+    Paths.get(getClass.getResource(p).toURI).toString
+
+  // Helper functions to create iterator over FastqRecords given its IDs as Ints
+  // Record with 'A' and Qual==39 (SangerEncoding)
+  private def recordsOver(ids: String*): java.util.Iterator[FastqRecord] = ids
+    .map(x => new FastqRecord(x, "A", "", "H"))
+    .toIterator.asJava
+
+  private def solexaRecordsOver(ids: String*): java.util.Iterator[FastqRecord] = ids
+    .map(x => new FastqRecord(x, "ACTGTNCGATAG", "", "abcde;ABCDEF"))
+    .toIterator.asJava
+
+  @DataProvider(name = "mockReaderProvider")
+  def mockReaderProvider() =
+    Array(
+      Array(mock[FastqReader])
+    )
+
+  @Test(dataProvider = "mockReaderProvider")
+  def testDefault(refMock: FastqReader) = {
+    when(refMock.iterator) thenReturn recordsOver("1", "2", "3")
+  }
+
+  @Test(dataProvider = "mockReaderProvider")
+  def testSeqCountReads(refMock: FastqReader) = {
+    when(refMock.iterator) thenReturn recordsOver("1", "2", "3", "4", "5")
+
+    val (numReads) = seqStat(refMock)
+    numReads shouldBe 5
+  }
+
+  @Test(dataProvider = "mockReaderProvider")
+  def testSeqQuality(refMock: FastqReader) = {
+    when(refMock.iterator) thenReturn recordsOver("1", "2", "3", "4", "5")
+
+    val (numReads) = seqStat(refMock)
+    numReads shouldBe 5
+  }
+
+  @Test(dataProvider = "mockReaderProvider")
+  def testEncodingDetectionSanger(refMock: FastqReader) = {
+    when(refMock.iterator) thenReturn recordsOver("1", "2", "3", "4", "5")
+
+    val (numReads) = seqStat(refMock)
+    numReads shouldBe 5
+
+    summarize()
+
+    phred_correction shouldBe 33
+    phred_encoding shouldBe "sanger"
+  }
+
+  @Test(dataProvider = "mockReaderProvider")
+  def testEncodingDetectionSolexa(refMock: FastqReader) = {
+    when(refMock.iterator) thenReturn solexaRecordsOver("1", "2", "3", "4", "5")
+
+    val (numReads) = seqStat(refMock)
+    numReads shouldBe 5
+
+    summarize()
+
+    phred_correction shouldBe 64
+    phred_encoding shouldBe "solexa"
+  }
+
+  @Test def testArgsMinimum() = {
+    val args = Array(
+      "-i", resourcePath("/paired01a.fq"))
+    val parsed = parseArgs(args)
+    parsed.fastq shouldBe resourceFile("/paired01a.fq")
+  }
+}
\ No newline at end of file