org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvsMnps 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.util.List;

import org.junit.Test;
import org.snpeff.snpEffect.commandLine.SnpEffCmdEff;
import org.snpeff.util.Gpr;
import org.snpeff.vcf.EffFormatVersion;
import org.snpeff.vcf.VcfEffect;
import org.snpeff.vcf.VcfEntry;

import junit.framework.Assert;

/**
 *
 * Test case
 */
public class TestCasesIntegrationHgvsMnps extends TestCasesIntegrationBase {

	public TestCasesIntegrationHgvsMnps() {
		super();
		shiftHgvs = true;
	}

	@Test
	public void test_01() {
		Gpr.debug("Test");
		String genome = "testHg19Chr17";
		String vcf = path("hgvs_mnps_01.vcf");
		compareHgvs(genome, vcf, false);
	}

	/**
	 * Test MNP simplification
	 */
	@Test
	public void test_02() {
		Gpr.debug("Test");

		String genome = "testHg19Chr17";
		String vcf = path("hgvs_mnps_02.vcf");

		// Create SnpEff
		String args[] = { genome, vcf };
		SnpEffCmdEff snpeff = new SnpEffCmdEff();
		snpeff.parseArgs(args);
		snpeff.setDebug(debug);
		snpeff.setVerbose(verbose);
		snpeff.setSupressOutput(!verbose);
		snpeff.setFormatVersion(EffFormatVersion.FORMAT_ANN_1);

		// Run & get result (single line)
		List results = snpeff.run(true);
		VcfEntry ve = results.get(0);

		// Check HGVS 'p.' notation
		boolean ok = false;
		for (VcfEffect veff : ve.getVcfEffects()) {
			if (verbose) Gpr.debug("\t" + veff + "\n\t\ttranscript: " + veff.getTranscriptId() + "\n\t\tHgvs (DNA): " + veff.getHgvsDna());
			if (veff.getTranscriptId().equals("NM_001042492.2")) {
				Assert.assertEquals("HGVS p. notation does not match", "p.Gln1055*", veff.getHgvsProt());
				ok = true;
			}
		}

		Assert.assertTrue("Transcript not found", ok);
	}

}