Commit 60d0fb74 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added testing for qiime biom to krona method

parent 6b8b3a37
......@@ -79,8 +79,6 @@ object GearsQiimeClosed {
val counts: mutable.Map[String, Long] = mutable.Map()
def totalCount(sample: String): Long = counts.getOrElse(sample, 0L) + childs.map(_.totalCount(sample)).sum
override def toString() = s"$level:$name:$counts"
def node: Elem = {
val sizes = sortedSamples.map { sample => <val>{ totalCount(sample) }</val> }
val size = <size>{ sizes }</size>
......
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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 GearsQiimeClosedTest extends TestNGSuite with Matchers {
private def resourcePath(p: String): String = {
Paths.get(getClass.getResource(p).toURI).toString
}
@Test
def testQiimeBiomToKrona: Unit = {
val qiimeBiomFile = new File(resourcePath("/otu_table.biom"))
val outputFile = File.createTempFile("krona.", ".xml")
outputFile.deleteOnExit()
GearsQiimeClosed.qiimeBiomToKrona(qiimeBiomFile, outputFile)
}
}
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