Skip to content

GitLab

Commit b10509f2 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Move shiva testing to public

parent d7b0ecdc
Hide whitespace changes
Inline Side-by-side
Showing with 35 additions and 190 deletions
protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala deleted 100644 → 0
View file @ d7b0ecdc
/**
* Due to the license issue with GATK, this part of Biopet can only be used inside the
* LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
* on how to use this protected part of biopet or contact us at sasc@lumc.nl
*/
package nl.lumc.sasc.biopet.pipelines.gatk
import java.io.{File, FileOutputStream}
import com.google.common.io.Files
import nl.lumc.sasc.biopet.utils.config.Config
import nl.lumc.sasc.biopet.extensions.bwa.BwaMem
import nl.lumc.sasc.biopet.extensions.gatk.broad._
import nl.lumc.sasc.biopet.extensions.picard.{MarkDuplicates, SortSam}
import nl.lumc.sasc.biopet.extensions.tools.VcfStats
import nl.lumc.sasc.biopet.pipelines.shiva.Shiva
import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.broadinstitute.gatk.queue.QSettings
import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite
import org.testng.annotations.{DataProvider, Test}
/**
* Class for testing shiva
*
* Created by pjvan_thof on 3/2/15.
*/
class ShivaTest extends TestNGSuite with Matchers {
def initPipeline(map: Map[String, Any]): Shiva = {
new Shiva() {
override def configNamespace = "shiva"
override def globalConfig = new Config(ConfigUtils.mergeMaps(map, ShivaTest.config))
qSettings = new QSettings
qSettings.runName = "test"
}
}
@DataProvider(name = "shivaOptions")
def shivaOptions = {
val bool = Array(true, false)
for (
s1 <- bool; s2 <- bool; multi <- bool;
dbsnp <- bool; realign <- bool; baseRecalibration <- bool
) yield Array("", s1, s2, multi, dbsnp, realign, baseRecalibration)
}
@Test(dataProvider = "shivaOptions")
def testShiva(f: String, sample1: Boolean, sample2: Boolean,
multi: Boolean, dbsnp: Boolean,
realign: Boolean, baseRecalibration: Boolean): Unit = {
val map = {
var m: Map[String, Any] = ShivaTest.config
if (sample1) m = ConfigUtils.mergeMaps(ShivaTest.sample1, m)
if (sample2) m = ConfigUtils.mergeMaps(ShivaTest.sample2, m)
if (dbsnp) m = ConfigUtils.mergeMaps(Map("dbsnp" -> "test.vcf.gz"), m)
ConfigUtils.mergeMaps(Map("multisample_variantcalling" -> multi,
"use_indel_realigner" -> realign,
"use_base_recalibration" -> baseRecalibration), m)
}
if (!sample1 && !sample2) { // When no samples
intercept[IllegalArgumentException] {
initPipeline(map).script()
}
} else {
val pipeline = initPipeline(map)
pipeline.script()
val numberLibs = (if (sample1) 1 else 0) + (if (sample2) 2 else 0)
val numberSamples = (if (sample1) 1 else 0) + (if (sample2) 1 else 0)
pipeline.functions.count(_.isInstanceOf[MarkDuplicates]) shouldBe (numberLibs + (if (sample2) 1 else 0))
// Gatk preprocess
pipeline.functions.count(_.isInstanceOf[IndelRealigner]) shouldBe (numberLibs * (if (realign) 1 else 0) + (if (sample2 && realign) 1 else 0))
pipeline.functions.count(_.isInstanceOf[RealignerTargetCreator]) shouldBe (numberLibs * (if (realign) 1 else 0) + (if (sample2 && realign) 1 else 0))
pipeline.functions.count(_.isInstanceOf[BaseRecalibrator]) shouldBe (if (dbsnp && baseRecalibration) numberLibs else 0)
pipeline.functions.count(_.isInstanceOf[PrintReads]) shouldBe (if (dbsnp && baseRecalibration) numberLibs else 0)
pipeline.functions.count(_.isInstanceOf[VcfStats]) shouldBe (if (multi) 2 else 0)
}
}
}
object ShivaTest {
val outputDir = Files.createTempDir()
new File(outputDir, "input").mkdirs()
def inputTouch(name: String): String = {
val file = new File(outputDir, "input" + File.separator + name)
Files.touch(file)
file.getAbsolutePath
}
private def copyFile(name: String): Unit = {
val is = getClass.getResourceAsStream("/" + name)
val os = new FileOutputStream(new File(outputDir, name))
org.apache.commons.io.IOUtils.copy(is, os)
os.close()
}
copyFile("ref.fa")
copyFile("ref.dict")
copyFile("ref.fa.fai")
val config = Map(
"name_prefix" -> "test",
"cache" -> true,
"dir" -> "test",
"vep_script" -> "test",
"output_dir" -> outputDir,
"reference_fasta" -> (outputDir + File.separator + "ref.fa"),
"gatk_jar" -> "test",
"samtools" -> Map("exe" -> "test"),
"bcftools" -> Map("exe" -> "test"),
"fastqc" -> Map("exe" -> "test"),
"input_alleles" -> "test",
"variantcallers" -> "raw",
"fastqc" -> Map("exe" -> "test"),
"seqtk" -> Map("exe" -> "test"),
"sickle" -> Map("exe" -> "test"),
"cutadapt" -> Map("exe" -> "test"),
"bwa" -> Map("exe" -> "test"),
"samtools" -> Map("exe" -> "test"),
"macs2" -> Map("exe" -> "test"),
"igvtools" -> Map("exe" -> "test"),
"wigtobigwig" -> Map("exe" -> "test"),
"md5sum" -> Map("exe" -> "test"),
"bgzip" -> Map("exe" -> "test"),
"tabix" -> Map("exe" -> "test")
)
val sample1 = Map(
"samples" -> Map("sample1" -> Map("libraries" -> Map(
"lib1" -> Map(
"R1" -> inputTouch("1_1_R1.fq"),
"R2" -> inputTouch("1_1_R2.fq")
)
)
)))
val sample2 = Map(
"samples" -> Map("sample3" -> Map("libraries" -> Map(
"lib1" -> Map(
"R1" -> inputTouch("2_1_R1.fq"),
"R2" -> inputTouch("2_1_R2.fq")
),
"lib2" -> Map(
"R1" -> inputTouch("2_2_R1.fq"),
"R2" -> inputTouch("2_2_R2.fq")
)
)
)))
}
\ No newline at end of file
public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
View file @ b10509f2
......@@ -15,24 +15,24 @@
*/
package nl.lumc.sasc.biopet.pipelines.shiva
import java.io.{ File, FileOutputStream }
import java.io.{File, FileOutputStream}
import com.google.common.io.Files
import nl.lumc.sasc.biopet.utils.config.Config
import nl.lumc.sasc.biopet.extensions.bwa.BwaMem
import nl.lumc.sasc.biopet.extensions.picard.{ MarkDuplicates, SortSam }
import nl.lumc.sasc.biopet.extensions.gatk.broad._
import nl.lumc.sasc.biopet.extensions.picard.MarkDuplicates
import nl.lumc.sasc.biopet.extensions.tools.VcfStats
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}
/**
* Test class for [[Shiva]]
*
* Created by pjvan_thof on 3/2/15.
*/
* Class for testing shiva
*
* Created by pjvan_thof on 3/2/15.
*/
class ShivaTest extends TestNGSuite with Matchers {
def initPipeline(map: Map[String, Any]): Shiva = {
new Shiva() {
......@@ -47,24 +47,28 @@ class ShivaTest extends TestNGSuite with Matchers {
def shivaOptions = {
val bool = Array(true, false)
for (s1 <- bool; s2 <- bool; s3 <- bool; multi <- bool; single <- bool; library <- bool)
yield Array("", s1, s2, s3, multi, single, library)
for (
s1 <- bool; s2 <- bool; multi <- bool;
dbsnp <- bool; realign <- bool; baseRecalibration <- bool
) yield Array("", s1, s2, multi, dbsnp, realign, baseRecalibration)
}
@Test(dataProvider = "shivaOptions")
def testShiva(f: String, sample1: Boolean, sample2: Boolean, sample3: Boolean,
multi: Boolean, single: Boolean, library: Boolean): Unit = {
def testShiva(f: String, sample1: Boolean, sample2: Boolean,
multi: Boolean, dbsnp: Boolean,
realign: Boolean, baseRecalibration: Boolean): Unit = {
val map = {
var m: Map[String, Any] = ShivaTest.config
if (sample1) m = ConfigUtils.mergeMaps(ShivaTest.sample1, m)
if (sample2) m = ConfigUtils.mergeMaps(ShivaTest.sample2, m)
if (sample3) m = ConfigUtils.mergeMaps(ShivaTest.sample3, m)
if (dbsnp) m = ConfigUtils.mergeMaps(Map("dbsnp" -> "test.vcf.gz"), m)
ConfigUtils.mergeMaps(Map("multisample_variantcalling" -> multi,
"single_sample_variantcalling" -> single,
"library_variantcalling" -> library), m)
"use_indel_realigner" -> realign,
"use_base_recalibration" -> baseRecalibration), m)
}
if (!sample1 && !sample2 && !sample3) { // When no samples
if (!sample1 && !sample2) { // When no samples
intercept[IllegalArgumentException] {
initPipeline(map).script()
}
......@@ -72,13 +76,18 @@ class ShivaTest extends TestNGSuite with Matchers {
val pipeline = initPipeline(map)
pipeline.script()
val numberLibs = (if (sample1) 1 else 0) + (if (sample2) 1 else 0) + (if (sample3) 2 else 0)
val numberSamples = (if (sample1) 1 else 0) + (if (sample2) 1 else 0) + (if (sample3) 1 else 0)
val numberLibs = (if (sample1) 1 else 0) + (if (sample2) 2 else 0)
val numberSamples = (if (sample1) 1 else 0) + (if (sample2) 1 else 0)
pipeline.functions.count(_.isInstanceOf[MarkDuplicates]) shouldBe (numberLibs + (if (sample2) 1 else 0))
pipeline.functions.count(_.isInstanceOf[MarkDuplicates]) shouldBe (numberLibs + (if (sample3) 1 else 0))
// Gatk preprocess
pipeline.functions.count(_.isInstanceOf[IndelRealigner]) shouldBe (numberLibs * (if (realign) 1 else 0) + (if (sample2 && realign) 1 else 0))
pipeline.functions.count(_.isInstanceOf[RealignerTargetCreator]) shouldBe (numberLibs * (if (realign) 1 else 0) + (if (sample2 && realign) 1 else 0))
pipeline.functions.count(_.isInstanceOf[BaseRecalibrator]) shouldBe (if (dbsnp && baseRecalibration) numberLibs else 0)
pipeline.functions.count(_.isInstanceOf[PrintReads]) shouldBe (if (dbsnp && baseRecalibration) numberLibs else 0)
pipeline.functions.count(_.isInstanceOf[VcfStats]) shouldBe (if (multi) 2 else 0) +
(if (single) numberSamples * 2 else 0) + (if (library) numberLibs * 2 else 0)
pipeline.functions.count(_.isInstanceOf[VcfStats]) shouldBe (if (multi) 2 else 0)
}
}
}
......@@ -105,10 +114,10 @@ object ShivaTest {
val config = Map(
"name_prefix" -> "test",
"output_dir" -> outputDir,
"cache" -> true,
"dir" -> "test",
"vep_script" -> "test",
"output_dir" -> outputDir,
"reference_fasta" -> (outputDir + File.separator + "ref.fa"),
"gatk_jar" -> "test",
"samtools" -> Map("exe" -> "test"),
......@@ -140,23 +149,14 @@ object ShivaTest {
)))
val sample2 = Map(
"samples" -> Map("sample2" -> Map("libraries" -> Map(
"samples" -> Map("sample3" -> Map("libraries" -> Map(
"lib1" -> Map(
"R1" -> inputTouch("2_1_R1.fq"),
"R2" -> inputTouch("2_1_R2.fq")
)
)
)))
val sample3 = Map(
"samples" -> Map("sample3" -> Map("libraries" -> Map(
"lib1" -> Map(
"R1" -> inputTouch("3_1_R1.fq"),
"R2" -> inputTouch("3_1_R2.fq")
),
"lib2" -> Map(
"R1" -> inputTouch("3_2_R1.fq"),
"R2" -> inputTouch("3_2_R2.fq")
"R1" -> inputTouch("2_2_R1.fq"),
"R2" -> inputTouch("2_2_R2.fq")
)
)
)))
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment