org.snpeff.snpEffect.testCases.unity.TestCasesDel 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.unity;

import org.junit.Before;
import org.junit.Test;
import org.snpeff.interval.BioType;
import org.snpeff.interval.Cds;
import org.snpeff.interval.Chromosome;
import org.snpeff.interval.Exon;
import org.snpeff.interval.Gene;
import org.snpeff.interval.Genome;
import org.snpeff.interval.Transcript;
import org.snpeff.interval.Variant;
import org.snpeff.snpEffect.Config;
import org.snpeff.snpEffect.EffectType;
import org.snpeff.snpEffect.SnpEffectPredictor;
import org.snpeff.snpEffect.VariantEffect;
import org.snpeff.snpEffect.VariantEffects;
import org.snpeff.util.GprSeq;

import junit.framework.Assert;

/**
 * Test random DEL changes
 *
 * @author pcingola
 */
public class TestCasesDel {

	public static int N = 1000;

	boolean debug = false;
	boolean verbose = false || debug;

	Config config;
	String chrSeq;
	Genome genome;
	Chromosome chr;
	Gene gene;
	Transcript tr;
	SnpEffectPredictor snpEffectPredictor;

	@Before
	public void init() {
		config = new Config("test");

		chrSeq = "CGTGTTACCAAGCATTTGGGAACCGGAATTCTACGCTGGAGTTCGCCTAACAGCTAAAGCTCAAAACAGGAGTGGTTTAGTTCACAGGCAGACCTTTAACGGTACCTACCTTAATCCGGTCAGATTTAAATTCATGATAGATGGTCTAAGTCATGCACTACTCCTACCAGTTTTGGACGTGGCGCATTGGGCCCCGACACCAAATGCGTTGGAGCGACAGCACAAACGATATCTCAGATTAAGTGCATTGAAGGCCTTCTCACGGATAGATCTATAGGTCGCTGTGTGTCGGGAAGTCTTTCATCCGCTCGGGAGTCGGGTAAATTCTTTCTTCCAGTTGTGTGTTCTACGACTGCAGAGGACAGCTCTCGCTTAGTTTCCTTCCGTTCTTTGTAAGGCCCGATAGGAATACCCGCATAATTATCCCCACAGTCTAACTTGATCCACGTCATATGGGGCGATGGCTGGAATGAGGGGGGTTCAGTGGCAGACCACGATATCTCTGTTTATCTGATGAAGAATTTTGGATACCCCAATAACTAATGTGAGAAGAGTGTGGGGTATCCAACGTGATTGGAGGGAAGTATGGAAACGAATGAAGACAAGTTCGACAAGCCGTGGTAACGATCATATGCCACCGTATTCTAACGGGGGGGGGCCGCTGTTTGAATGCCAGATAGATATTTAAAGAGGATGGCCGCCCCCCAATGGGCACGAGGAACTGACCAGAGGTAGGTATGATGGTGTGAGAGAGAGATGTAGTGTAGTTACTATAAAGATTTGAAGATCGAAAGGCTTAGTGATACGAAACCTCCCGCTACTGCGGGCCGGTATAGCAGGTCTAATACTTGGTGATAGGGCTACATCGAGCCTCGTTCGACAAGAATACCCCAGTTGCAATGGGGACCGATTCAGTCTGGGGCTCTGTGGTCCGACATTATGCCGGAATGCCTAGTATGGGAATTAAAACGATTAATATTACCTCTGGGACTATCTTTGTGCCAAACTCTACTGAGAGAGGAACGTAATCGTATTAGGGGCCAAGATAGTTTACTCCGATCCACCGTAACACTTATTTTGGGCCGTGCGTACCCACCCACGGTCATGAACGCAAACTGGATAGGGCGCGTCATACGAGCTAAAGTGTTCTCTTGGGGCAAATAAGAAGGGACTAGCTGTATTCCCCTCCCATTGTGTGGGTACAATTCGGGGGAAAGGTGTCGAGCCCAAATGCTACGGCTCGTAGATATCAGGTCCTTTAGCCGCCCGTATGTAAGCACCTCCAACGTTTTGGAGGAAGATCCCTCTCCCACGGGTTATACCATTAATGACTCCGCACTAACAATATCTTACCAGGGCCCGCAAATACCACACCGGGATACTGGAATGAATTATTCTCCGACCCATTTGATGAAACGTATGGGAACTTTCCTGTTGTATTAAACCCGCGGATACACTCTCTTGCCCACGAGTAGCCTCTACTTACTAGATTGAGAGGTACACTACGCCATTATGAAGCATTTCGACTTTCACTCCAGTATATAGAAGGTATGTGTGGATCCTTCAAAATAGTGATCCGAACCTGGTTGTAGGGGCCACCGAAATTCCGATTACTGAAGATTAATGTTTTCAAATGCCCTATTTCACTGGTGATAGCGATGGAGCCGGGCTATCATCATGGCGAAGCACGTGGGAAAGCATTCCGTCAAGGCTAGTGGGAACCTCTGCCTTGCCATGTACGCGTTCTATATACACGAACATCGATACCGGTCTCGTCCTGGGGTAGAGCCATCCTCATCACGAGTGATGTAGGACGGCTAGCTCATTAATTCACTGCGTGTCAGATAGAATGTCTTCGTGCGCAAAAATTGTTTAGGAGACCGTCGGCGCTCCCTTGGAGAGATGCCCAACGTAGAGAGGCAATCCCCGGCGTATTGGTGGTTTCTGGAACGGAACGAGACTCTTTGTTGCGTCGACTCCCGGCAACACCGGCCCCCGCCG";
		genome = new Genome("test");

		chr = new Chromosome(genome, 0, chrSeq.length() - 1, "1");
		chr.setSequence(chrSeq);
		genome.add(chr);

		gene = new Gene(chr, 333, 408, true, "gene1", "gene1", BioType.protein_coding);

		tr = new Transcript(gene, 333, 408, true, "tr1");
		gene.add(tr);
		tr.setProteinCoding(true);

		Exon e1 = new Exon(tr, 333, 334, true, "exon1", 0);
		Exon e2 = new Exon(tr, 353, 364, true, "exon2", 0);
		Exon e3 = new Exon(tr, 388, 398, true, "exon3", 0);
		Exon e4 = new Exon(tr, 404, 408, true, "exon4", 0);
		Exon exons[] = { e1, e2, e3, e4 };

		for (Exon e : exons) {
			String seq = chrSeq.substring(e.getStart(), e.getEnd() + 1);
			seq = GprSeq.reverseWc(seq);
			e.setSequence(seq);
			tr.add(e);

			Cds cds = new Cds(tr, e.getStart(), e.getEnd(), e.isStrandMinus(), "");
			tr.add(cds);
		}
		tr.rankExons();

		if (verbose) System.out.println("Transcript:\n" + tr);
		Assert.assertEquals("FLPYKAVLCR", tr.protein());

		snpEffectPredictor = new SnpEffectPredictor(genome);
		snpEffectPredictor.setUpDownStreamLength(0);
		snpEffectPredictor.add(gene);
		snpEffectPredictor.buildForest();
	}

	@Test
	public void test_01() {
		// Create variant
		Variant var = new Variant(chr, 397, "GCCCGATAGGA", "", "");
		if (verbose) System.out.println("Variant: " + var + "\n" + tr.toStringAsciiArt(true));
		Assert.assertEquals("chr1:397_GCCCGATAGGA/", var.toString());

		// Calculate effects
		int countMatch = 0;
		VariantEffects effectsAll = snpEffectPredictor.variantEffect(var);
		for (VariantEffect eff : effectsAll) {
			if (verbose) System.out.println("\t" + eff);
			if (eff.getEffectType() == EffectType.CODON_CHANGE_PLUS_CODON_DELETION) {
				if (verbose) System.out.println("\t" + eff.getEffectTypeString(false) + "\t" + eff.getCodonsRef() + "\t" + eff.getCodonsAlt());
				Assert.assertEquals("TCT", eff.getCodonsAlt().toUpperCase());
				countMatch++;
			}
		}

		Assert.assertTrue("No variant effects found", countMatch > 0);
	}

	@Test
	public void test_02() {
		// Create variant
		int start = 300;
		Variant var = new Variant(chr, start, chrSeq.substring(300, 450), "", "");
		if (verbose) System.out.println("Transcript:" + tr + "\nVariant: " + var);

		// Calculate effects
		int countMatch = 0;
		VariantEffects effectsAll = snpEffectPredictor.variantEffect(var);
		for (VariantEffect eff : effectsAll) {
			if (verbose) System.out.println("\t" + eff.getEffectTypeString(false) + "\tHGVS.p: '" + eff.getHgvsProt() + "'");
			if (eff.getEffectType() == EffectType.TRANSCRIPT_DELETED) {
				countMatch++;
				Assert.assertEquals("HGVS.p notation error", "p.0?", eff.getHgvsProt());
			}
		}
		Assert.assertTrue("No variant effects found", countMatch > 0);
	}
}