org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse2 Maven / Gradle / Ivy

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Variant annotation and effect prediction package.

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package org.snpeff.snpEffect.testCases.unity;

import org.junit.Assert;
import org.junit.Test;
import org.snpeff.interval.Gene;
import org.snpeff.interval.Genome;
import org.snpeff.interval.SpliceSite;
import org.snpeff.interval.Variant;
import org.snpeff.snpEffect.VariantEffect;
import org.snpeff.snpEffect.VariantEffects;
import org.snpeff.util.Gpr;
import org.snpeff.vcf.EffFormatVersion;
import org.snpeff.vcf.VcfEffect;

/**
 * Test case
 */
public class TestCasesEffectCollapse2 extends TestCasesBase {

	public TestCasesEffectCollapse2() {
		super();
	}

	@Override
	protected void init() {
		super.init();
		randSeed = 20150202;
		spliceRegionExonSize = SpliceSite.SPLICE_REGION_EXON_SIZE;
		spliceRegionIntronMin = SpliceSite.SPLICE_REGION_INTRON_MIN;
		spliceRegionIntronMax = SpliceSite.SPLICE_REGION_INTRON_MAX;
		maxExons = 10;
		minExons = 5;
		addUtrs = true;
		onlyPlusStrand = true;
	}

	@Test
	public void test_01() {
		Gpr.debug("Test");

		// Show gene(s)
		Genome genome = snpEffectPredictor.getGenome();
		if (verbose) {
			for (Gene g : genome.getGenes())
				System.out.println(g);
		}

		// Create variant
		Variant variant = new Variant(genome.getChromosome("1"), 695, "ACGTACGTACGTACGT", "");
		if (verbose) System.out.println(variant.getVariantType() + "\t" + variant.getStart() + "-" + variant.getEnd() + "\t" + variant);

		// Calculate effect
		VariantEffects veffs = snpEffectPredictor.variantEffect(variant);

		// Look for expected annotations
		String expectedAnn = "5_prime_UTR_truncation&exon_loss_variant";
		boolean foundSo = false;
		boolean foundAnn = false;
		for (VariantEffect veff : veffs) {
			VcfEffect vcfEff = new VcfEffect(veff, EffFormatVersion.FORMAT_ANN_1);
			if (verbose) System.out.println(vcfEff.getEffectsStrSo() + "\t" + vcfEff);

			foundSo |= vcfEff.getEffectsStrSo().equalsIgnoreCase(expectedAnn);
			foundAnn |= vcfEff.toString().indexOf(expectedAnn) >= 0;
		}

		// Annotation found?
		Assert.assertTrue("Annotation (SO) '" + expectedAnn + "' not found", foundSo);
		Assert.assertTrue("Annotation '" + expectedAnn + "' not found in 'ANN' field", foundAnn);
	}

}