org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationSnp 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.SnpEff;
import org.snpeff.snpEffect.EffectType;
import org.snpeff.snpEffect.VariantEffect.EffectImpact;
import org.snpeff.snpEffect.commandLine.SnpEffCmdEff;
import org.snpeff.util.Gpr;
import org.snpeff.vcf.VcfEffect;
import org.snpeff.vcf.VcfEntry;

import junit.framework.Assert;

/**
 * Test SNP variants
 *
 * @author pcingola
 */
public class TestCasesIntegrationSnp extends TestCasesIntegrationBase {

	/**
	 * Change of start codon to an alternative start codon
	 */
	@Test
	public void test_02_Start_NonSyn() {
		Gpr.debug("Test");
		String genome = "testHg19ChrM";
		String vcf = path("test_chrM_start_codon_nonSyn.vcf");

		String args[] = { "-noLog", "-classic", "-ud", "0", genome, vcf };
		SnpEff snpEff = new SnpEff(args);
		snpEff.setVerbose(verbose);
		snpEff.setSupressOutput(!verbose);
		snpEff.setDebug(debug);

		SnpEffCmdEff seff = (SnpEffCmdEff) snpEff.cmd();
		boolean checked = false;
		List vcfEntries = seff.run(true);
		for (VcfEntry ve : vcfEntries) {
			if (verbose) System.out.println(ve);
			for (VcfEffect veff : ve.getVcfEffects()) {
				if (verbose) System.out.println("\t\t" + veff);
				if (veff.getEffectType() == EffectType.NON_SYNONYMOUS_START) {
					Assert.assertEquals(EffectImpact.LOW, veff.getImpact());
					checked = true;
				}
			}
		}
		Assert.assertEquals(true, checked);

	}

	/**
	 * Stop gained should have 'HIGH' impact
	 */
	@Test
	public void test_02_StopGained_HighImpact() {
		Gpr.debug("Test");
		String genome = "testHg3775Chr2";
		String vcf = path("stop_gained_chr2.vcf");

		String args[] = { "-noLog", "-classic", genome, vcf };
		SnpEff snpEff = new SnpEff(args);
		snpEff.setVerbose(verbose);
		snpEff.setSupressOutput(!verbose);
		snpEff.setDebug(debug);

		SnpEffCmdEff seff = (SnpEffCmdEff) snpEff.cmd();
		boolean checked = false;
		List vcfEntries = seff.run(true);
		for (VcfEntry ve : vcfEntries) {
			if (verbose) System.out.println(ve);
			for (VcfEffect veff : ve.getVcfEffects()) {
				if (verbose) System.out.println("\t\t" + veff);
				if (veff.getEffectType() == EffectType.STOP_GAINED) {
					Assert.assertEquals(EffectImpact.HIGH, veff.getImpact());
					checked = true;
				}
			}
		}

		Assert.assertEquals(true, checked);
	}

	/**
	 * Change of start codon to an alternative start codon
	 */
	@Test
	public void test_03_Start_Loss() {
		Gpr.debug("Test");
		String genome = "testHg19ChrM";
		String vcf = path("test_chrM_start_codon.vcf");

		String args[] = { "-noLog", "-classic", "-ud", "0", genome, vcf };
		SnpEff snpEff = new SnpEff(args);
		snpEff.setVerbose(verbose);
		snpEff.setSupressOutput(!verbose);
		snpEff.setDebug(debug);

		SnpEffCmdEff seff = (SnpEffCmdEff) snpEff.cmd();
		boolean checked = false;
		List vcfEntries = seff.run(true);
		for (VcfEntry ve : vcfEntries) {
			if (verbose) System.out.println(ve);
			for (VcfEffect veff : ve.getVcfEffects()) {
				if (verbose) System.out.println("\t\t" + veff);
				if (veff.getEffectType() == EffectType.START_LOST) {
					Assert.assertEquals(EffectImpact.HIGH, veff.getImpact());
					checked = true;
				}
			}
		}
		Assert.assertEquals(true, checked);

	}

}