From 51141a2739a27bd01e7f7cae6feb542b348d1986 Mon Sep 17 00:00:00 2001
From: Sander Bollen <a.h.b.bollen@lumc.nl>
Date: Mon, 13 Apr 2015 17:31:26 +0200
Subject: [PATCH] Adding tests for VcfToTsv
---
.../lumc/sasc/biopet/tools/VcfToTsvTest.scala | 70 +++++++++++++++++++
1 file changed, 70 insertions(+)
create mode 100644 public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfToTsvTest.scala
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfToTsvTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfToTsvTest.scala
new file mode 100644
index 000000000..598f4550d
--- /dev/null
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfToTsvTest.scala
@@ -0,0 +1,70 @@
+package nl.lumc.sasc.biopet.tools
+
+import java.nio.file.Paths
+import java.util
+import scala.collection.JavaConversions._
+
+import org.scalatest.Matchers
+import org.scalatest.mock.MockitoSugar
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+import scala.util.Random
+
+/**
+ * Created by ahbbollen on 13-4-15.
+ */
+class VcfToTsvTest extends TestNGSuite with MockitoSugar with Matchers {
+ import VcfToTsv._
+ private def resourcePath(p: String): String = {
+ Paths.get(getClass.getResource(p).toURI).toString
+ }
+
+ val rand = new Random()
+
+ val vepped = resourcePath("/VEP_oneline.vcf")
+ val unvepped = resourcePath("/unvepped.vcf")
+
+ @Test def testAllFields() = {
+ val tmp_path = "/tmp/VcfToTsv_" + rand.nextString(10) + ".tsv"
+ val arguments = Array("-I", unvepped, "-o", tmp_path, "--all_info")
+ main(arguments)
+ }
+
+ @Test def testSpecificField() = {
+ val tmp_path = "/tmp/VcfToTsv_" + rand.nextString(10) + ".tsv"
+ val arguments = Array("-I", vepped, "-o", tmp_path, "-i", "CSQ")
+ main(arguments)
+ }
+
+ @Test def testNewSeparators() = {
+ val tmp_path = "/tmp/VcfToTsv_" + rand.nextString(10) + ".tsv"
+ val arguments = Array("-I", vepped, "-o", tmp_path, "--all_info", "--separator", ",", "--list_separator", "|")
+ main(arguments)
+ }
+
+ @Test(expectedExceptions = Array(classOf[IllegalArgumentException]))
+ def testIdenticalSeparators() = {
+ val tmp_path = "/tmp/VcfToTsv_" + rand.nextString(10) + ".tsv"
+ val arguments = Array("-I", vepped, "-o", tmp_path, "--all_info", "--separator", ",")
+ main(arguments)
+ }
+
+ @Test def testFormatter() = {
+ val formatter = createFormatter(2)
+ formatter.format(5000.12345) should be("5000.12")
+ val nformatter = createFormatter(3)
+ nformatter.format(5000.12345) should be("5000.123")
+ }
+
+ @Test def testSortFields() = {
+ val unsortedFields = Set("Child01-GT", "Mother02-GT", "Father03-GT", "INFO-Something", "INFO-ScoreSomething",
+ "INFO-AlleleScoreSomething", "WeirdField")
+ val samples = List("Child01", "Father03", "Mother02")
+
+ val sorted = sortFields(unsortedFields, samples)
+ sorted should be(List("WeirdField", "INFO-AlleleScoreSomething", "INFO-ScoreSomething", "INFO-Something",
+ "Child01-GT", "Father03-GT", "Mother02-GT"))
+ }
+
+}
--
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