From 497eef6f590e633bc4c570da0902daf832b5eb4b Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Thu, 5 Mar 2015 18:43:15 +0100
Subject: [PATCH] Initial update for GentrapTest
---
.../pipelines/gentrap/GentrapTest.scala | 120 +++++++++++++-----
1 file changed, 86 insertions(+), 34 deletions(-)
diff --git a/public/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala b/public/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
index 0e2485219..4a789611c 100644
--- a/public/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
+++ b/public/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
@@ -4,50 +4,102 @@
*/
package nl.lumc.sasc.biopet.pipelines.gentrap
+import java.io.File
+
+import com.google.common.io.Files
+import org.apache.commons.io.FileUtils
+import org.broadinstitute.gatk.queue.QSettings
import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite
-import org.testng.annotations.Test
+import org.testng.annotations.{ AfterClass, DataProvider, Test }
import nl.lumc.sasc.biopet.core.config.Config
+import nl.lumc.sasc.biopet.extensions._
+import nl.lumc.sasc.biopet.pipelines.gentrap.extensions._
+import nl.lumc.sasc.biopet.pipelines.gentrap.scripts._
+import nl.lumc.sasc.biopet.tools.{ MergeTables, WipeReads }
+import nl.lumc.sasc.biopet.utils.ConfigUtils
class GentrapTest extends TestNGSuite with Matchers {
- /** Method to set test config */
- // since the pipeline Config is a global value, we first store the
- // initial config into a value, store the supplied value, then return
- // the initial config for restoring later
- private def setConfig(map: Map[String, Any]): Map[String, Any] = {
- val oldMap: Map[String, Any] = Config.global.map.toMap
- Config.global.map = map
- oldMap
+ def initPipeline(map: Map[String, Any]): Gentrap = {
+ new Gentrap() {
+ override def configName = "gentrap"
+ override def globalConfig = new Config(map)
+ qSettings = new QSettings
+ qSettings.runName = "test"
+ }
}
- /** Method to set the global config */
- private def restoreConfig(initConfig: Map[String, Any]): Unit = Config.global.map = initConfig
-
- /** Minimum config required for Gentrap */
- private val minimumConfig = Map(
- "output_dir" -> "/tmp",
- "aligner" -> "gsnap",
- "expression_measures" -> List(),
- "strand_protocol" -> "non_specific",
- "reference" -> "mock",
- "gsnap" -> Map("db" -> "fixt_gentrap_hg19"),
- "samples" -> Map(
- "sample_1" -> Map(
- "libraries" -> Map(
- "lib_1" -> Map(
- "R1" -> "/tmp/mock.fq"
+ private lazy val validExpressionMeasures = Set(
+ "fragments_per_gene", "fragments_per_exon", "bases_per_gene", "bases_per_exon",
+ "cufflinks_strict", "cufflinks_guided", "cufflinks_blind")
+
+ @DataProvider(name = "gentrapOptions")
+ def flexiprepOptions = {
+
+ //val paired = Array(true, false)
+ val paired = Array(false)
+ val expressionMeasures = validExpressionMeasures
+ .subsets
+ .map(_.toList)
+ .toArray
+
+ for (
+ pair <- paired;
+ expressionMeasure <- expressionMeasures
+ ) yield Array("", pair, expressionMeasure)
+ }
+
+ @Test(dataProvider = "gentrapOptions")
+ def testGentrap(name: String, paired: Boolean, expMeasures: List[String]) = {
+
+ val map = ConfigUtils.mergeMaps(
+ Map(
+ "output_dir" -> GentrapTest.outputDir,
+ "gsnap" -> Map("db" -> "test", "dir" -> "test"),
+ "aligner" -> "gsnap",
+ "expression_measures" -> expMeasures,
+ "strand_protocol" -> "non_specific",
+ "samples" -> Map(
+ "sample_1" -> Map(
+ "libraries" -> Map(
+ "lib_1" -> Map(
+ "R1" -> "test_R1.fq"
+ )
+ )
)
)
- )
- )
- )
-
- // Test pipeline initialization with minimum config -- there should be no exceptions raised
- @Test def testInitMinimumConfig() = {
- val initialConfig = setConfig(minimumConfig)
- val gentrap = new Gentrap()
- restoreConfig(initialConfig)
+ ),
+ Map(GentrapTest.executables.toSeq: _*))
+ val gentrap: Gentrap = initPipeline(map)
+
+ gentrap.script()
+
+ gentrap.functions.count(_.isInstanceOf[Gsnap]) shouldBe 1
+ }
+
+ // remove temporary run directory all tests in the class have been run
+ @AfterClass def removeTempOutputDir() = {
+ FileUtils.deleteDirectory(GentrapTest.outputDir)
}
}
+
+object GentrapTest {
+ val outputDir = Files.createTempDir()
+
+ val executables = Map(
+ "reference" -> "test",
+ "annotation_gtf" -> "test",
+ "annotation_bed" -> "test",
+ "annotation_refflat" -> "test",
+ "stampy" -> Map("exe" -> "test", "genome" -> "test", "hash" -> "test")
+ ) ++ Seq(
+ // fastqc executables
+ "fastqc", "seqtk", "sickle", "cutadapt",
+ // mapping executables
+ "bwa", "star", "bowtie", "samtools", "gsnap",
+ // gentrap executables
+ "cufflinks", "htseq-count", "grep", "pdflatex", "Rscript", "tabix", "bgzip"
+ ).map { case exe => exe -> Map("exe" -> "test") }.toMap
+}
--
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