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Commit 6b8b3a37 authored by Peter van 't Hof's avatar Peter van 't Hof
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Added testing for kraken to krona method

parent 768f5596
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public/gears/src/test/resources/hpv_simu_R1.krkn.json 0 → 100644
View file @ 6b8b3a37
{
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"size" : 732,
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"taxonrank" : "U"
},
"classified" : {
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"children" : [
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"name" : "Human herpesvirus 4 type 2",
"count" : 6,
"taxid" : 12509,
"size" : 6,
"cladelevel" : 8,
"taxonrank" : "-"
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],
"name" : "Human herpesvirus 4",
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"size" : 3908,
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"taxonrank" : "S"
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],
"name" : "Lymphocryptovirus",
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"taxid" : 10375,
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"cladelevel" : 6,
"taxonrank" : "G"
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],
"name" : "Gammaherpesvirinae",
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{
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"name" : "Cytomegalovirus",
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"cladelevel" : 6,
"taxonrank" : "G"
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],
"name" : "Betaherpesvirinae",
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"name" : "Herpesviridae",
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"taxid" : 10292,
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"cladelevel" : 4,
"taxonrank" : "F"
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"name" : "Herpesvirales",
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"taxid" : 548681,
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],
"name" : "dsDNA viruses, no RNA stage",
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"taxid" : 35237,
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"cladelevel" : 2,
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],
"name" : "Viruses",
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public/gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsKrakenTest.scala 0 → 100644
View file @ 6b8b3a37
package nl.lumc.sasc.biopet.pipelines.gears
import java.io.File
import java.nio.file.Paths
import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite
import org.testng.annotations.Test
/**
* Created by pjvan_thof on 2/5/16.
*/
class GearsKrakenTest extends TestNGSuite with Matchers {
private def resourcePath(p: String): String = {
Paths.get(getClass.getResource(p).toURI).toString
}
@Test
def testConvertKrakenJsonToKronaXml: Unit = {
val krakenJsonFile = new File(resourcePath("/hpv_simu_R1.krkn.json"))
val outputFile = File.createTempFile("krona.", ".xml")
outputFile.deleteOnExit()
GearsKraken.convertKrakenJsonToKronaXml(Map("test" -> krakenJsonFile), outputFile)
}
}
public/gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsTest.scala
View file @ 6b8b3a37
......@@ -9,11 +9,11 @@ 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.{DataProvider, Test, AfterClass}
import org.testng.annotations.{ DataProvider, Test, AfterClass }
/**
* Created by pjvanthof on 04/02/16.
*/
* Created by pjvanthof on 04/02/16.
*/
class GearsTest extends TestNGSuite with Matchers {
def initPipeline(map: Map[String, Any]): Gears = {
new Gears {
......@@ -35,7 +35,6 @@ class GearsTest extends TestNGSuite with Matchers {
) yield Array("", s1, s2, qiimeClosed)
}
@Test(dataProvider = "gearsOptions")
def testGears(dummy: String, sample1: Boolean, sample2: Boolean, qiimeCLosed: Boolean): Unit = {
val map = {
......@@ -53,7 +52,6 @@ class GearsTest extends TestNGSuite with Matchers {
val pipeline = initPipeline(map)
pipeline.script()
}
}
......
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