From 6894dd4dbe8fb41653dfd1d5074f060380946828 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 11 Apr 2016 09:45:48 +0200
Subject: [PATCH] Adding test to GensToVcf
---
.../src/test/resources/gens.samples | 5 ++
.../biopet-tools/src/test/resources/test.gens | 3 ++
.../src/test/resources/test.gens_info | 4 ++
.../sasc/biopet/tools/GensToVcfTest.scala | 48 +++++++++++++++++++
4 files changed, 60 insertions(+)
create mode 100644 public/biopet-tools/src/test/resources/gens.samples
create mode 100644 public/biopet-tools/src/test/resources/test.gens
create mode 100644 public/biopet-tools/src/test/resources/test.gens_info
create mode 100644 public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/GensToVcfTest.scala
diff --git a/public/biopet-tools/src/test/resources/gens.samples b/public/biopet-tools/src/test/resources/gens.samples
new file mode 100644
index 000000000..1789a409e
--- /dev/null
+++ b/public/biopet-tools/src/test/resources/gens.samples
@@ -0,0 +1,5 @@
+ID_1 ID_2 missing hip knee hand knee_or_hip sex age bmi
+0 0 0 D D D D D P P
+sample-1 fam-1 0.0 2 NA 2 2 1 59.0767123287671 27.1314117909924
+sample-2 fam-1 0.0 2 NA NA 2 2 48.4958904109589 23.8754325259516
+sample-3 fam-1 0.0 NA NA NA NA 2 57.0876712328767 45.8842609074008
diff --git a/public/biopet-tools/src/test/resources/test.gens b/public/biopet-tools/src/test/resources/test.gens
new file mode 100644
index 000000000..bec79dab8
--- /dev/null
+++ b/public/biopet-tools/src/test/resources/test.gens
@@ -0,0 +1,3 @@
+--- rs1 30 A C 1 0 0 0 1 0 0 0 1
+--- rs2 40 A - 1 0 0 0 1 0 0 0 1
+--- rs3 50 A AT 1 0 0 0 1 0 0 0 1
\ No newline at end of file
diff --git a/public/biopet-tools/src/test/resources/test.gens_info b/public/biopet-tools/src/test/resources/test.gens_info
new file mode 100644
index 000000000..250a9677f
--- /dev/null
+++ b/public/biopet-tools/src/test/resources/test.gens_info
@@ -0,0 +1,4 @@
+snp_id rs_id position exp_freq_a1 info certainty type info_type0 concord_type0 r2_type0
+--- rs1 30 0.037 0.535 0.958 0 -1 -1 -1
+--- rs2 40 0.023 0.621 0.978 0 -1 -1 -1
+--- rs3 50 0.000 0.114 0.999 0 -1 -1 -1
diff --git a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/GensToVcfTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/GensToVcfTest.scala
new file mode 100644
index 000000000..01a196a79
--- /dev/null
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/GensToVcfTest.scala
@@ -0,0 +1,48 @@
+package nl.lumc.sasc.biopet.tools
+
+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 4/11/16.
+ */
+class GensToVcfTest extends TestNGSuite with Matchers {
+ @Test
+ def testGensOnly: Unit = {
+ val output = File.createTempFile("test.", ".vcf.gz")
+ GensToVcf.main(Array(
+ "--inputGenotypes", GensToVcfTest.resourcePath("/test.gens"),
+ "--outputVcf", output.getAbsolutePath,
+ "--referenceFasta", GensToVcfTest.resourcePath("/fake_chrQ.fa"),
+ "--contig", "chrQ",
+ "--samplesFile", GensToVcfTest.resourcePath("/gens.samples")
+ ))
+ }
+
+ @Test
+ def testGensInfo: Unit = {
+ val output = File.createTempFile("test.", ".vcf.gz")
+ GensToVcf.main(Array(
+ "--inputGenotypes", GensToVcfTest.resourcePath("/test.gens"),
+ "--inputInfo", GensToVcfTest.resourcePath("/test.gens_info"),
+ "--outputVcf", output.getAbsolutePath,
+ "--referenceFasta", GensToVcfTest.resourcePath("/fake_chrQ.fa"),
+ "--contig", "chrQ",
+ "--samplesFile", GensToVcfTest.resourcePath("/gens.samples"),
+ "--sortInput"
+ ))
+ }
+
+}
+
+object GensToVcfTest {
+ private def resourcePath(p: String): String = {
+ Paths.get(getClass.getResource(p).toURI).toString
+ }
+
+
+}
--
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