org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvs 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.EffectType;
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 random SNP changes
 *
 * @author pcingola
 */
public class TestCasesIntegrationHgvs extends TestCasesIntegrationBase {

	@Test
	public void test_02() {
		Gpr.debug("Test");

		String genomeName = "testHg3775Chr1";
		String vcf = path("hgvs_1.vep.vcf");
		CompareToVep comp = new CompareToVep(genomeName, verbose);
		comp.setCompareHgvs();
		comp.compareVep(vcf);
		if (verbose) System.out.println(comp);
		Assert.assertTrue("No comparissons were made!", comp.checkComapred());
	}

	@Test
	public void test_03() {
		Gpr.debug("Test");
		String genomeName = "testHg3775Chr1";
		String vcf = path("ensembl_hgvs_intron.1.vep.vcf");
		CompareToVep comp = new CompareToVep(genomeName, verbose);
		comp.setCompareHgvs();
		comp.setStrict(true);
		comp.setOnlyProtein(true);
		comp.compareVep(vcf);
		if (verbose) System.out.println(comp);
		Assert.assertTrue("No comparissons were made!", comp.checkComapred());
	}

	@Test
	public void test_04() {
		Gpr.debug("Test");
		String genomeName = "testHg3775Chr1";
		String vcf = path("ensembl_hgvs_intron.outsideCds.vep.vcf");
		CompareToVep comp = new CompareToVep(genomeName, verbose);
		comp.setCompareHgvs();
		comp.setStrict(true);
		comp.setOnlyProtein(true);
		comp.compareVep(vcf);
		if (verbose) System.out.println(comp);
		Assert.assertTrue("No comparissons were made!", comp.checkComapred());
	}

	@Test
	public void test_05() {
		Gpr.debug("Test");
		String genomeName = "testHg3775Chr1";
		String vcf = path("ensembl_hgvs_intron.vep.vcf");
		CompareToVep comp = new CompareToVep(genomeName, verbose);
		comp.setCompareHgvs();
		comp.setStrict(true);
		comp.setOnlyProtein(true);
		comp.compareVep(vcf);
		if (verbose) System.out.println(comp);
		Assert.assertTrue("No comparissons were made!", comp.checkComapred());
	}

	@Test
	public void test_06() {
		Gpr.debug("Test");
		String genomeName = "testHg3775Chr1";
		String vcf = path("ensembl_hgvs_intron.within_cds.vep.vcf");
		CompareToVep comp = new CompareToVep(genomeName, verbose);
		comp.setCompareHgvs();
		comp.setStrict(true);
		comp.setOnlyProtein(true);
		comp.compareVep(vcf);
		if (verbose) System.out.println(comp);
		Assert.assertTrue("No comparissons were made!", comp.checkComapred());
	}

	@Test
	public void test_10_MixedVep_HGVS() {
		Gpr.debug("Test");
		String genome = "testHg3775Chr1";
		String vcf = path("mixed_10_hgvs.vep.vcf");
		CompareToVep comp = new CompareToVep(genome, verbose);
		comp.setCompareHgvs();
		comp.setOnlyProtein(true);
		comp.compareVep(vcf);
		if (verbose) System.out.println(comp);
		Assert.assertTrue("No comparissons were made!", comp.checkComapred());
	}

	@Test
	public void test_11_Hg19Hgvs() {
		Gpr.debug("Test");

		String genome = "testHg19Hgvs";
		String vcf = path("hgvs_counsyl.vcf");
		CompareToVep comp = new CompareToVep(genome, verbose);
		comp.setCompareHgvs();
		comp.setCompareHgvsProt(false);
		comp.setShiftHgvs(true);
		comp.compareVep(vcf);
		if (verbose) System.out.println(comp);
		Assert.assertTrue("No comparissons were made!", comp.checkComapred());
	}

	@Test
	public void test_11_Hg19Hgvs_noShift() {
		Gpr.debug("Test");
		String genome = "testHg19Hgvs";
		String vcf = path("hgvs_counsyl.noShift.vcf");
		CompareToVep comp = new CompareToVep(genome, verbose);
		comp.setCompareHgvs();
		comp.setCompareHgvsProt(false);
		comp.setShiftHgvs(false);
		comp.compareVep(vcf);
		if (verbose) System.out.println(comp);
		Assert.assertTrue("No comparissons were made!", comp.checkComapred());
	}

	/**
	 * Using non-standard splice size (15 instead of 2)
	 * may cause some HGVS annotations issues
	 */
	@Test
	public void test_12_BRCA_Splice_15_Hgvs() {
		Gpr.debug("Test");
		int spliceSize = 15;
		String genome = "test_BRCA";
		String vcf = path("test_BRCA_splice_15.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);

		// The problem appears when splice site is large (in this example)
		snpeff.setSpliceSiteSize(spliceSize);
		snpeff.setUpDownStreamLength(0);
		snpeff.setShiftHgvs(false);

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

		// Make sure the spleice site is annotatted as "c.1909+12delT" (instead of "c.1910delT")
		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());
			ok |= veff.getTranscriptId().equals("ENST00000544455") && veff.getHgvsDna().equals("c.1909+12delT");
		}

		Assert.assertTrue(ok);
	}

	/**
	 * Using non-standard splice size (15 instead of 2)
	 * may cause some HGVS annotations issues
	 */
	@Test
	public void test_14_splice_region_Hgvs() {
		Gpr.debug("Test");
		String genome = "testHg19Chr1";
		String vcf = path("hgvs_splice_region.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);

		// The problem appears when splice site is large (in this example)
		snpeff.setUpDownStreamLength(0);

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

		// Make sure the spleice site is annotatted as "c.1909+12delT" (instead of "c.1910delT")
		boolean ok = false;
		for (VcfEffect veff : ve.getVcfEffects()) {
			if (verbose) System.out.println("\t" + veff + "\t" + veff.getEffectsStr() + "\t" + veff.getHgvsDna());
			ok |= veff.hasEffectType(EffectType.SPLICE_SITE_REGION) //
					&& veff.getTranscriptId().equals("NM_001232.3") //
					&& veff.getHgvsDna().equals("c.420+6T>C");
		}

		Assert.assertTrue(ok);
	}

	/**
	 * Using non-standard splice size (15 instead of 2)
	 * may cause some HGVS annotations issues
	 */
	@Test
	public void test_15_hgvs_INS_intergenic() {
		Gpr.debug("Test");
		String genome = "testHg3775Chr22";
		String vcf = path("test_hgvs_INS_intergenic.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);

		// Make sure the HCVGs annotaion is correct
		boolean ok = false;
		for (VcfEffect veff : ve.getVcfEffects()) {
			if (verbose) System.out.println("\t" + veff + "\t" + veff.getEffectsStr() + "\t" + veff.getHgvsDna());
			ok |= veff.hasEffectType(EffectType.INTERGENIC) //
					&& veff.getHgvsDna().equals("n.15070000_15070001insT") //
			;
		}

		Assert.assertTrue("Error in HGVS annotaiton", ok);
	}

}