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

Go to download

Show more of this group Show more artifacts with this name
Show all versions of SnpEff Show documentation

Variant annotation and effect prediction package.

The newest version!

package org.snpeff.snpEffect.testCases.integration;

import java.util.List;

import org.junit.Assert;
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;

/**
 * Test random SNP changes
 *
 * @author pcingola
 */
public class TestCasesIntegrationHgvsLarge extends TestCasesIntegrationBase {

	/**
	 * Using non-standard splice size (15 instead of 2)
	 * may cause some HGVS annotations issues
	 */
	@Test
	public void test_13_large_Del_Hgvs() {
		Gpr.debug("Test");
		String genome = "testHg3775Chr22";
		String vcf = path("test_large_del_hgvs_13.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_EFF_4);

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

		// Make sure HGVS string is not so long
		for (VcfEffect veff : ve.getVcfEffects()) {
			if (verbose) System.out.println(veff);

			if (verbose) System.out.println("\tAA change    : " + veff.getAa());
			Assert.assertTrue(veff.getAa() == null || veff.getAa().length() < 100);

			if (verbose) System.out.println("\tCodon change : " + veff.getCodon());
			Assert.assertTrue(veff.getCodon() == null || veff.getCodon().length() < 100);

		}
	}

}