From 2a90688756e6e461dcf105107b82e1f619d822a1 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 12 Feb 2015 16:09:33 +0100
Subject: [PATCH] Added flexiprep testing
---
.../pipelines/flexiprep/FlexiprepTest.scala | 155 ++++++++++++++++++
1 file changed, 155 insertions(+)
create mode 100644 public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala
diff --git a/public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala b/public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala
new file mode 100644
index 000000000..e3953235e
--- /dev/null
+++ b/public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala
@@ -0,0 +1,155 @@
+package nl.lumc.sasc.biopet.pipelines.flexiprep
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.config.Config
+import nl.lumc.sasc.biopet.extensions.{ Gzip, Zcat }
+import nl.lumc.sasc.biopet.tools.FastqSync
+import nl.lumc.sasc.biopet.utils.ConfigUtils
+import org.broadinstitute.gatk.queue.QSettings
+import org.broadinstitute.gatk.queue.function.QFunction
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+/**
+ * Created by pjvan_thof on 2/11/15.
+ */
+class FlexiprepTest extends TestNGSuite with Matchers {
+
+ def initPipeline(map: Map[String, Any]): Flexiprep = {
+ new Flexiprep() {
+ override def configName = "flexiprep"
+ override def globalConfig = new Config(map)
+ qSettings = new QSettings
+ qSettings.runName = "test." + System.currentTimeMillis
+ }
+ }
+
+ @Test def TestDefault = {
+ val map = ConfigUtils.mergeMaps(Map("output_dir" -> FlexiprepTest.outputDir), Map(FlexiprepTest.excutables.toSeq: _*))
+ val flexiprep: Flexiprep = initPipeline(map)
+
+ flexiprep.input_R1 = new File(flexiprep.outputDir, "bla.fq")
+ flexiprep.sampleId = "1"
+ flexiprep.libId = "1"
+ flexiprep.script()
+
+ flexiprep.functions.count(_.isInstanceOf[Fastqc]) shouldBe 2
+ flexiprep.functions.count(_.isInstanceOf[Zcat]) shouldBe 0
+ flexiprep.functions.count(_.isInstanceOf[SeqtkSeq]) shouldBe 1
+ flexiprep.functions.count(_.isInstanceOf[Cutadapt]) shouldBe 1
+ flexiprep.functions.count(_.isInstanceOf[FastqSync]) shouldBe 0
+ flexiprep.functions.count(_.isInstanceOf[Sickle]) shouldBe 1
+ flexiprep.functions.count(_.isInstanceOf[Gzip]) shouldBe 1
+ }
+
+ @Test def TestDefaultPaired = {
+ val map = ConfigUtils.mergeMaps(Map("output_dir" -> FlexiprepTest.outputDir), Map(FlexiprepTest.excutables.toSeq: _*))
+ val flexiprep: Flexiprep = initPipeline(map)
+
+ flexiprep.input_R1 = new File(flexiprep.outputDir, "bla_R1.fq.gz")
+ flexiprep.input_R2 = Some(new File(flexiprep.outputDir, "bla_R2.fq.gz"))
+ flexiprep.sampleId = "1"
+ flexiprep.libId = "1"
+ flexiprep.script()
+
+ flexiprep.functions.count(_.isInstanceOf[Fastqc]) shouldBe 4
+ flexiprep.functions.count(_.isInstanceOf[Zcat]) shouldBe 2
+ flexiprep.functions.count(_.isInstanceOf[SeqtkSeq]) shouldBe 2
+ flexiprep.functions.count(_.isInstanceOf[Cutadapt]) shouldBe 2
+ flexiprep.functions.count(_.isInstanceOf[FastqSync]) shouldBe 1
+ flexiprep.functions.count(_.isInstanceOf[Sickle]) shouldBe 1
+ flexiprep.functions.count(_.isInstanceOf[Gzip]) shouldBe 2
+ }
+
+ @Test def TestClipTrimPaired = {
+ val map = ConfigUtils.mergeMaps(Map("output_dir" -> FlexiprepTest.outputDir, "skip_trim" -> false, "skip_clip" -> false),
+ Map(FlexiprepTest.excutables.toSeq: _*))
+ val flexiprep: Flexiprep = initPipeline(map)
+
+ flexiprep.input_R1 = new File(flexiprep.outputDir, "bla_R1.fq.gz")
+ flexiprep.input_R2 = Some(new File(flexiprep.outputDir, "bla_R2.fq.gz"))
+ flexiprep.sampleId = "1"
+ flexiprep.libId = "1"
+ flexiprep.script()
+
+ flexiprep.functions.count(_.isInstanceOf[Fastqc]) shouldBe 4
+ flexiprep.functions.count(_.isInstanceOf[Zcat]) shouldBe 2
+ flexiprep.functions.count(_.isInstanceOf[SeqtkSeq]) shouldBe 2
+ flexiprep.functions.count(_.isInstanceOf[Cutadapt]) shouldBe 2
+ flexiprep.functions.count(_.isInstanceOf[FastqSync]) shouldBe 1
+ flexiprep.functions.count(_.isInstanceOf[Sickle]) shouldBe 1
+ flexiprep.functions.count(_.isInstanceOf[Gzip]) shouldBe 2
+ }
+
+ @Test def TestTrimPaired = {
+ val map = ConfigUtils.mergeMaps(Map("output_dir" -> FlexiprepTest.outputDir, "skip_trim" -> false, "skip_clip" -> true),
+ Map(FlexiprepTest.excutables.toSeq: _*))
+ val flexiprep: Flexiprep = initPipeline(map)
+
+ flexiprep.input_R1 = new File(flexiprep.outputDir, "bla_R1.fq.gz")
+ flexiprep.input_R2 = Some(new File(flexiprep.outputDir, "bla_R2.fq.gz"))
+ flexiprep.sampleId = "1"
+ flexiprep.libId = "1"
+ flexiprep.script()
+
+ flexiprep.functions.count(_.isInstanceOf[Fastqc]) shouldBe 4
+ flexiprep.functions.count(_.isInstanceOf[Zcat]) shouldBe 2
+ flexiprep.functions.count(_.isInstanceOf[SeqtkSeq]) shouldBe 2
+ flexiprep.functions.count(_.isInstanceOf[Cutadapt]) shouldBe 0
+ flexiprep.functions.count(_.isInstanceOf[FastqSync]) shouldBe 0
+ flexiprep.functions.count(_.isInstanceOf[Sickle]) shouldBe 1
+ flexiprep.functions.count(_.isInstanceOf[Gzip]) shouldBe 2
+ }
+
+ @Test def TestClipPaired = {
+ val map = ConfigUtils.mergeMaps(Map("output_dir" -> FlexiprepTest.outputDir, "skip_trim" -> true, "skip_clip" -> false),
+ Map(FlexiprepTest.excutables.toSeq: _*))
+ val flexiprep: Flexiprep = initPipeline(map)
+
+ flexiprep.input_R1 = new File(flexiprep.outputDir, "bla_R1.fq.gz")
+ flexiprep.input_R2 = Some(new File(flexiprep.outputDir, "bla_R2.fq.gz"))
+ flexiprep.sampleId = "1"
+ flexiprep.libId = "1"
+ flexiprep.script()
+
+ flexiprep.functions.count(_.isInstanceOf[Fastqc]) shouldBe 4
+ flexiprep.functions.count(_.isInstanceOf[Zcat]) shouldBe 2
+ flexiprep.functions.count(_.isInstanceOf[SeqtkSeq]) shouldBe 2
+ flexiprep.functions.count(_.isInstanceOf[Cutadapt]) shouldBe 2
+ flexiprep.functions.count(_.isInstanceOf[FastqSync]) shouldBe 1
+ flexiprep.functions.count(_.isInstanceOf[Sickle]) shouldBe 0
+ flexiprep.functions.count(_.isInstanceOf[Gzip]) shouldBe 2
+ }
+
+ @Test def TestPaired = {
+ val map = ConfigUtils.mergeMaps(Map("output_dir" -> FlexiprepTest.outputDir, "skip_trim" -> true, "skip_clip" -> true),
+ Map(FlexiprepTest.excutables.toSeq: _*))
+ val flexiprep: Flexiprep = initPipeline(map)
+
+ flexiprep.input_R1 = new File(flexiprep.outputDir, "bla_R1.fq.gz")
+ flexiprep.input_R2 = Some(new File(flexiprep.outputDir, "bla_R2.fq.gz"))
+ flexiprep.sampleId = "1"
+ flexiprep.libId = "1"
+ flexiprep.script()
+
+ flexiprep.functions.count(_.isInstanceOf[Fastqc]) shouldBe 2
+ flexiprep.functions.count(_.isInstanceOf[Zcat]) shouldBe 2
+ flexiprep.functions.count(_.isInstanceOf[SeqtkSeq]) shouldBe 2
+ flexiprep.functions.count(_.isInstanceOf[Cutadapt]) shouldBe 0
+ flexiprep.functions.count(_.isInstanceOf[FastqSync]) shouldBe 0
+ flexiprep.functions.count(_.isInstanceOf[Sickle]) shouldBe 0
+ flexiprep.functions.count(_.isInstanceOf[Gzip]) shouldBe 2
+ }
+}
+object FlexiprepTest {
+ val outputDir = System.getProperty("java.io.tmpdir") + File.separator + "flexiprep"
+
+ val excutables = Map(
+ "seqstat" -> Map("exe" -> "test"),
+ "fastqc" -> Map("exe" -> "test"),
+ "seqtk" -> Map("exe" -> "test"),
+ "sickle" -> Map("exe" -> "test")
+ )
+}
\ No newline at end of file
--
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