org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationSequenceOntology Maven / Gradle / Ivy

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Variant annotation and effect prediction package.

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package org.snpeff.snpEffect.testCases.integration;

import java.io.IOException;

import org.junit.Test;
import org.snpeff.util.Gpr;

/**
 *
 * Test case for sequence ontology
 *
 * @author pcingola
 */
public class TestCasesIntegrationSequenceOntology extends TestCasesIntegrationBase {

	public TestCasesIntegrationSequenceOntology() {
		super();
	}

	@Test
	public void test_01_Vep() throws IOException {
		Gpr.debug("Test");
		compareVepSO("testENST00000268124", path("testENST00000268124.SNP.vcf"), "ENST00000268124");
	}

	@Test
	public void test_02_Vep() throws IOException {
		Gpr.debug("Test");
		compareVepSO("testENST00000268124", path("testENST00000268124.SNP.02.vcf"), "ENST00000268124");
	}

	@Test
	public void test_03_Vep() throws IOException {
		Gpr.debug("Test");
		compareVepSO("testENST00000268124", path("testENST00000268124.Ins.03.vcf"), "ENST00000268124");
	}

	@Test
	public void test_04_Vep() throws IOException {
		Gpr.debug("Test");
		compareVepSO("testENST00000398332", path("testENST00000398332.Ins.04.vcf"), "ENST00000398332");
	}

	@Test
	public void test_05_Vep() throws IOException {
		Gpr.debug("Test");
		compareVepSO("testENST00000268124", path("testENST00000268124.Del.05.vcf"), "ENST00000268124");
	}

	@Test
	public void test_06_Vep() throws IOException {
		Gpr.debug("Test");
		compareVepSO("testENST00000268124", path("testENST00000268124.Mnp.06.vcf"), "ENST00000268124");
	}

}