org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationGtf22 Maven / Gradle / Ivy

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Variant annotation and effect prediction package.

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package org.snpeff.snpEffect.testCases.integration;

import org.junit.After;
import org.junit.Before;
import org.junit.Test;
import org.snpeff.interval.Exon;
import org.snpeff.util.Gpr;

/**
 * Test case for GTF22 file parsing
 *
 * @author pcingola
 */
public class TestCasesIntegrationGtf22 extends TestCasesIntegrationBase {

	int exonToStringVersionOri;

	public TestCasesIntegrationGtf22() {
		super();
	}

	@After
	public void after() {
		Exon.ToStringVersion = exonToStringVersionOri;
	}

	@Before
	public void before() {
		exonToStringVersionOri = Exon.ToStringVersion;
		Exon.ToStringVersion = 1; // Set "toString()" version
	}

	@Test
	public void testCaseHg37_61_ENST00000250838() {
		Gpr.debug("Test");
		String genome = "testHg37.61";
		String gtfFile = path("ENST00000250838.gtf");
		String fastaFile = path("chrY.fa.gz");
		String resultFile = path("ENST00000250838.txt");
		buildGtfAndCompare(genome, gtfFile, fastaFile, resultFile);
	}

	@Test
	public void testCaseHg37_61_ENST00000331397() {
		Gpr.debug("Test");
		String genome = "testHg37.61";
		String gtfFile = path("ENST00000331397.gtf22");
		String fastaFile = path("chrY.fa.gz");
		String resultFile = path("ENST00000331397.txt");
		buildGtfAndCompare(genome, gtfFile, fastaFile, resultFile);
	}

	@Test
	public void testCaseMm37_61_ENSMUSG00000051951() {
		Gpr.debug("Test");
		String genome = "testMm37.61";
		String gtfFile = path("ENSMUSG00000051951.gtf");
		String resultFile = path("ENSMUSG00000051951.txt");
		buildGtfAndCompare(genome, gtfFile, null, resultFile);
	}

	@Test
	public void testCaseMm37_61_ENSMUST00000070533() {
		Gpr.debug("Test");
		String genome = "testMm37.61";
		String gtfFile = path("ENSMUST00000070533.gtf");
		String resultFile = path("ENSMUST00000070533.txt");
		buildGtfAndCompare(genome, gtfFile, null, resultFile);
	}

}