From 3ef511a0f0036d7d0cbe13ce3f59e97119aedea7 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 21 Jun 2016 11:04:23 +0200
Subject: [PATCH] Added testing for aligner in gentrap
---
.../pipelines/gentrap/GentrapTest.scala | 36 +++++++++++++------
1 file changed, 25 insertions(+), 11 deletions(-)
diff --git a/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala b/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
index a981f4e48..34e093691 100644
--- a/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
+++ b/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
@@ -14,19 +14,21 @@
*/
package nl.lumc.sasc.biopet.pipelines.gentrap
-import java.io.{ File, FileOutputStream }
+import java.io.{File, FileOutputStream}
import com.google.common.io.Files
import nl.lumc.sasc.biopet.extensions._
+import nl.lumc.sasc.biopet.extensions.gmap.Gsnap
+import nl.lumc.sasc.biopet.extensions.hisat.Hisat2
import nl.lumc.sasc.biopet.extensions.tools.BaseCounter
import nl.lumc.sasc.biopet.utils.ConfigUtils
import nl.lumc.sasc.biopet.utils.config.Config
import org.broadinstitute.gatk.queue.QSettings
import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite
-import org.testng.annotations.{ DataProvider, Test }
+import org.testng.annotations.{DataProvider, Test}
-abstract class GentrapTestAbstract(val expressionMeasure: String) extends TestNGSuite with Matchers {
+abstract class GentrapTestAbstract(val expressionMeasure: String, val aligner: Option[String]) extends TestNGSuite with Matchers {
def initPipeline(map: Map[String, Any]): Gentrap = {
new Gentrap() {
@@ -105,10 +107,9 @@ abstract class GentrapTestAbstract(val expressionMeasure: String) extends TestNG
val settings = Map(
"output_dir" -> GentrapTest.outputDir,
"gsnap" -> Map("db" -> "test", "dir" -> "test"),
- "aligner" -> "gsnap",
"expression_measures" -> expMeasures,
"strand_protocol" -> strandProtocol
- )
+ ) ++ aligner.map("aligner" -> _)
val config = ConfigUtils.mergeMaps(settings ++ sampleConfig, Map(GentrapTest.executables.toSeq: _*))
val gentrap: Gentrap = initPipeline(config)
@@ -139,16 +140,29 @@ abstract class GentrapTestAbstract(val expressionMeasure: String) extends TestNG
assert(gentrap.functions.exists(_.isInstanceOf[Cufflinks]))
assert(gentrap.functions.exists(_.isInstanceOf[Ln]))
}
+
+ val classMap = Map(
+ "gsnap" -> classOf[Gsnap],
+ "tophat" -> classOf[Tophat],
+ "star" -> classOf[Star],
+ "star-2pass" -> classOf[Star],
+ "hisat2" -> classOf[Hisat2]
+ )
+
+ val alignerClass = classMap.get(aligner.getOrElse("gsnap"))
+
+ alignerClass.foreach(c => assert(gentrap.functions.exists(c.isInstance(_))))
+ classMap.values.filterNot(Some(_) == alignerClass).foreach(x => assert(!gentrap.functions.exists(x.isInstance(_))))
}
}
-class GentrapFragmentsPerGeneTest extends GentrapTestAbstract("fragments_per_gene")
-//class GentrapFragmentsPerExonTest extends GentrapTestAbstract("fragments_per_exon")
-class GentrapBaseCountsTest extends GentrapTestAbstract("base_counts")
-class GentrapCufflinksStrictTest extends GentrapTestAbstract("cufflinks_strict")
-class GentrapCufflinksGuidedTest extends GentrapTestAbstract("cufflinks_guided")
-class GentrapCufflinksBlindTest extends GentrapTestAbstract("cufflinks_blind")
+class GentrapFragmentsPerGeneTest extends GentrapTestAbstract("fragments_per_gene", None)
+//class GentrapFragmentsPerExonTest extends GentrapTestAbstract("fragments_per_exon", None)
+class GentrapBaseCountsTest extends GentrapTestAbstract("base_counts", Some("gsnap"))
+class GentrapCufflinksStrictTest extends GentrapTestAbstract("cufflinks_strict", None)
+class GentrapCufflinksGuidedTest extends GentrapTestAbstract("cufflinks_guided", None)
+class GentrapCufflinksBlindTest extends GentrapTestAbstract("cufflinks_blind", None)
object GentrapTest {
val outputDir = Files.createTempDir()
--
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