org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationEff 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.Test;
import org.snpeff.snpEffect.VariantEffect.EffectImpact;
import org.snpeff.util.Gpr;
import org.snpeff.vcf.VcfEffect;
import org.snpeff.vcf.VcfEntry;

import junit.framework.Assert;

/**
 *
 * Test cases for other 'effect' issues
 *
 * @author pcingola
 */
public class TestCasesIntegrationEff extends TestCasesIntegrationBase {

	public TestCasesIntegrationEff() {
		super();
	}

	/**
	 * Test output order
	 */
	@Test
	public void test_01() {
		Gpr.debug("Test");
		List vcfEntries = snpEffect("testHg3770Chr22", path("eff_sort.vcf"), null);

		for (VcfEntry ve : vcfEntries) {
			if (verbose) System.out.println(ve);

			EffectImpact impPrev = EffectImpact.HIGH;
			for (VcfEffect veff : ve.getVcfEffects()) {
				EffectImpact imp = veff.getImpact();

				if (verbose) System.out.println("\t" + imp + "\t" + impPrev + "\t" + imp.compareTo(impPrev) + "\t" + veff);
				Assert.assertTrue(impPrev.compareTo(imp) <= 0); // Higher impact go first
				impPrev = imp;
			}
		}
	}

	/**
	 * Test output order: Canonical first
	 */
	@Test
	public void test_01_canonical() {
		Gpr.debug("Test");
		List vcfEntries = snpEffect("testHg3775Chr8", path("eff_sort_canon.vcf"), null);

		// Only one entry in this file
		Assert.assertEquals(1, vcfEntries.size());

		VcfEntry ve = vcfEntries.get(0);
		VcfEffect veff = ve.getVcfEffects().get(0);

		Assert.assertEquals("ENST00000456015", veff.getTranscriptId());
	}

	/**
	 * Test GATK option: At most one effect per VCF entry
	 */
	@Test
	public void test_02() {
		Gpr.debug("Test");
		String args[] = { "-o", "gatk" };
		List vcfEntries = snpEffect("testHg3770Chr22", path("eff_sort.vcf"), args);

		for (VcfEntry ve : vcfEntries) {
			int numEffs = ve.getVcfEffects().size();
			if (verbose) System.out.println("Num effects:" + numEffs + "\t" + ve);
			Assert.assertTrue(numEffs <= 1);
		}
	}

	/**
	 * Make sure that empty VCF does not trigger an exception when creating the summary
	 */
	@Test
	public void test_03_EmptyVcf() {
		Gpr.debug("Test");
		String args[] = { "eff", "-noLog" };
		snpEffect("testHg3770Chr22", path("empty_only_header.vcf"), args);
	}

	/**
	 * Test that CSV summary does not throw any error
	 */
	@Test
	public void test_04() {
		Gpr.debug("Test");
		String args[] = { "-csvStats", "test_04_TestCasesEff.csv" };
		snpEffect("testHg3770Chr22", path("eff_sort.vcf"), args);
	}

	/**
	 * GATK mode should not have SPLICE_REGION (it is currently not supported)
	 */
	@Test
	public void test_05() {
		Gpr.debug("Test");
		String genomeName = "testHg3775Chr1";
		String vcf = path("gatk_NO_splice_regions.vcf");
		String args[] = { "eff", "-noLog", "-o", "gatk" };
		List vcfEntries = snpEffect(genomeName, vcf, args);

		for (VcfEntry ve : vcfEntries) {
			if (verbose) System.out.println(ve);

			for (VcfEffect veff : ve.getVcfEffects()) {
				if (verbose) System.out.println("\t'" + veff.getEffectsStr() + "'\t" + veff);
				if (veff.getEffectsStr().indexOf("SPLICE_SITE_REGION") >= 0) throw new RuntimeException("Splice region effects should not present in GATK compatible mode");
			}
		}
	}

	/**
	 * Test an MNP at the end of the transcript: We should be able to annotate without throwing any error
	 */
	@Test
	public void test_06() {
		Gpr.debug("Test");
		String args[] = {};
		List list = snpEffect("testHg3775Chr15", path("mnp_insertion_at_transcript_end.vcf"), args);

		// We should be able to annotate this entry (if INFO is empty, something went wrong)
		Assert.assertFalse(list.get(0).getInfoStr().isEmpty());
	}

	/**
	 * Test an MNP at the end of the transcript: We should be able to annotate without throwing any error
	 */
	@Test
	public void test_07() {
		Gpr.debug("Test");
		String args[] = {};
		List list = snpEffect("testHg3775Chr10", path("mnp_deletion.vcf"), args);

		// We should be able to annotate this entry (if INFO is empty, something went wrong)
		Assert.assertFalse(list.get(0).getInfoStr().isEmpty());
	}

	/**
	 * Fixing bug: GATK does not annotate all VCF entries
	 */
	@Test
	public void test_08_gatk_missing_annotations() {
		Gpr.debug("Test");

		String genomeName = "testMycobacterium_tuberculosis_CCDC5079_uid203790";
		String vcf = path("test_gatk_no_annotations.vcf");
		String args[] = { "-noLog", "-o", "gatk" };
		List vcfEntries = snpEffect(genomeName, vcf, args);

		for (VcfEntry ve : vcfEntries) {
			int count = 0;
			if (verbose) System.out.println(ve);

			for (VcfEffect veff : ve.getVcfEffects()) {
				if (verbose) System.out.println("\t'" + veff.getEffectsStr() + "'\t" + veff);
				count++;
			}

			// Check that there is one and only one annotation
			Assert.assertEquals(1, count);
		}
	}

}