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

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Variant annotation and effect prediction package.
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package org.snpeff.snpEffect.testCases.integration;

import org.junit.Assert;
import org.junit.Test;
import org.snpeff.interval.Chromosome;
import org.snpeff.interval.Gene;
import org.snpeff.interval.Genome;
import org.snpeff.interval.Transcript;
import org.snpeff.interval.Variant;
import org.snpeff.snpEffect.SnpEffectPredictor;
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 TestCasesIntegrationCircularGenome extends TestCasesIntegrationBase {

	public TestCasesIntegrationCircularGenome() {
		super();
	}

	@Test
	public void testCase_01_CircularGenome() {
		Gpr.debug("Test");

		// Create database & build interval forest
		String genomeName = "testCase";
		String genBankFile = path("genes_circular.gbk");
		SnpEffectPredictor sep = buildGeneBank(genomeName, genBankFile);
		sep.buildForest();

		// Create variant
		Genome genome = sep.getGenome();
		Variant var = new Variant(genome.getChromosome("chr"), 2, "", "TATTTTTCAG", "");

		// Calculate effect
		// This should NOT throw an exception ("Interval has negative coordinates.")
		VariantEffects varEffs = sep.variantEffect(var);
		for (VariantEffect varEff : varEffs) {
			VcfEffect vcfEff = new VcfEffect(varEff, EffFormatVersion.FORMAT_ANN_1);
			if (verbose) System.out.println("\t" + vcfEff);
		}
	}

	@Test
	public void testCase_02_CircularGenome() {
		Gpr.debug("Test");

		//---
		// Create database & build interval forest
		//---
		String genomeName = "test_circular_GCA_000210475.1.22";
		SnpEffectPredictor sep = build(genomeName);
		sep.buildForest();

		if (verbose) {
			Genome genome = sep.getGenome();
			for (Chromosome chr : genome.getChromosomes())
				System.out.println(chr);
		}

		// Check if chr is circular
		Chromosome chr = sep.getGenome().getChromosome("p948");
		if (verbose) System.out.println("Chromosome:" + chr);
		Assert.assertTrue("Chromosome is not circular", chr.isCircular());

		// Check protien sequence
		String protein = "MDTSLAHENARLRALLQTQQDTIRQMAEYNRLLSQRVAAYASEINRLKALVAKLQRMQFGKSSEKLRAKTERQIQEAQERISALQEEMAETLGEQYDPVLPSALRQSSARKPLPASLPRETRVIRPEEECCPACGGELSSLGCDVSEQLELISSAFKVIETQRPKQACCRCDHIVQAPVPSKPIARSYAGAGLLAHVVTGKYADHLPLYRQSEIYRRQGVELSRATLGRWTGAVAELLEPLYDVLRQYVLMPGKVHADDIPVPVQEPGSGKTRTARLWVYVRDDRNAGSQMPPAVWFAYSPDRKGIHPQNHLAGYSGVLQADAYGGYRALYESGRITEAACMAHARRKIHDVHARAPTYITTEALQRIGELYAIEAEVRGCSAEQRLAARKARAAPLMQSLYDWIQQQMKTLSRHSDTAKAFAYLLKQWDALNVYCSNGWVEIDNNIAENALRGVAVGRKNWMFAGSDSGGEHAAVLYSLIGTCRLNNVEPEKWLRYVIEHIQDWPANRVRDLLPWKVDLSSQ*";
		for (Gene g : sep.getGenome().getGenes()) {
			for (Transcript tr : g) {
				Assert.assertEquals("Expected protein sequence does not match", protein, tr.protein());
				if (verbose) System.out.println(tr);
			}
		}

		//---
		// Check variants in zero or negative coordiantes
		//---
		checkAnnotations(sep, "p948", 0, "T", "A", "p.Phe297Ile", "c.889T>A", "missense_variant");
		checkAnnotations(sep, "p948", -3, "T", "A", "p.Trp296Arg", "c.886T>A", "missense_variant");
		checkAnnotations(sep, "p948", -885, "G", "T", "p.Asp2Tyr", "c.4G>T", "missense_variant");

		//---
		// Check variant after chromosome end (same variants as before)
		//---
		checkAnnotations(sep, "p948", 94797, "T", "A", "p.Phe297Ile", "c.889T>A", "missense_variant");
		checkAnnotations(sep, "p948", 94794, "T", "A", "p.Trp296Arg", "c.886T>A", "missense_variant");
		checkAnnotations(sep, "p948", 93912, "G", "T", "p.Asp2Tyr", "c.4G>T", "missense_variant");
	}

	@Test
	public void testCase_02_CircularGenome_end() {
		Gpr.debug("Test");

		//---
		// Create database & build interval forest
		//---
		String genomeName = "test_circular_GCA_000210475.1.22_end";
		SnpEffectPredictor sep = build(genomeName);
		sep.buildForest();

		if (verbose) {
			Genome genome = sep.getGenome();
			for (Chromosome chr : genome.getChromosomes())
				System.out.println(chr);
		}

		//---
		// Check variants in zero or negative coordinates
		//---
		checkAnnotations(sep, "p948", 0, "T", "A", "p.Phe297Ile", "c.889T>A", "missense_variant");
		checkAnnotations(sep, "p948", -3, "T", "A", "p.Trp296Arg", "c.886T>A", "missense_variant");
		checkAnnotations(sep, "p948", -885, "G", "T", "p.Asp2Tyr", "c.4G>T", "missense_variant");

		//---
		// Check variant after chromosome end (same variants as before)
		//---
		checkAnnotations(sep, "p948", 94797, "T", "A", "p.Phe297Ile", "c.889T>A", "missense_variant");
		checkAnnotations(sep, "p948", 94794, "T", "A", "p.Trp296Arg", "c.886T>A", "missense_variant");
		checkAnnotations(sep, "p948", 93912, "G", "T", "p.Asp2Tyr", "c.4G>T", "missense_variant");
	}

	@Test
	public void testCase_03_CircularGenome() {
		Gpr.debug("Test");

		String prot = "MQTECSAGAYEFPASCGRRVVARFDGGRMSSDGGVILVKQADDILGLSRRF" //
				+ "AACFRDKRHPGFVEYIPQSRDAAYRENRQQSGG*" //
		;

		String cds = "ATGCAGACAGAGTGTAGCGCAGGCGCGTATGAGTTTCCAGCCTCCTGTGGAC" //
				+ "GGCGTGTTGTGGCCCGTTTTGACGGGGGTCGCATGAGTTCGGATGGGGGCGTCAT" //
				+ "TCTGGTGAAGCAGGCTGATGACATTCTGGGTCTCAGCCGCCGCTTTGCTGCCTGT" //
				+ "TTTCGCGATAAGCGGCATCCCGGCTTTGTGGAATATATTCCACAAAGCCGGGATG" //
				+ "CCGCTTATCGCGAAAACAGGCAGCAAAGCGGCGGCTGA" //
		;

		// Create database & build interval forest
		String genomeName = "test_Acetobacter_pasteurianus";
		SnpEffectPredictor sep = build(genomeName);
		Gene g = sep.getGene("DB34_00005");
		Transcript tr = g.subIntervals().iterator().next();
		Assert.assertEquals("Protein sequence differs", prot, tr.protein());
		Assert.assertEquals("CDS sequence differs", cds, tr.cds().toUpperCase());
	}

	@Test
	public void testCase_04_CircularGenome() {
		Gpr.debug("Test");

		String prot = "MTNNIVIAGRLVADAELFFTNNGSAICNFTLANNKRYKDIEKSTFIEASIFGNYAESMNK" //
				+ "YLKKGVSIDVIGELVQESWSKDGKIYYKHKIKVKEIDFRTPKDNISEANFENEDTPSNHL" //
				+ "LYLVEDNMRAVTIPIIISEQTPNIAKFSNVISKECKLSLAICSMVLLLSSIIFNHIQPSY" //
				+ "SKSSIQIFVKTTPNKNAITYIARNPTNSSIINNSLLVLICKLCILWQFIIYYYIHSL*" //
		;

		String cds = "ATGACAAATAATATAGTAATTGCAGGAAGATTGGTGGCAGACGCTGAACTATTTTTTACA" //
				+ "AATAATGGCTCTGCTATTTGTAATTTTACTTTGGCGAATAATAAAAGATACAAAGACATA" //
				+ "GAAAAAAGCACTTTTATAGAAGCTAGTATTTTTGGCAACTATGCAGAATCTATGAATAAG" //
				+ "TATCTAAAAAAAGGCGTATCAATTGATGTAATAGGAGAGCTGGTTCAAGAAAGCTGGAGC" //
				+ "AAAGATGGAAAAATATATTATAAACATAAAATCAAAGTCAAAGAGATTGATTTTAGAACA" //
				+ "CCAAAAGATAATATTTCAGAAGCAAACTTTGAAAATGAAGATACACCCTCAAATCATCTG" //
				+ "CTTTATCTGGTGGAAGACAATATGAGAGCTGTAACTATTCCTATTATCATAAGTGAGCAA" //
				+ "ACGCCAAATATAGCAAAATTCTCAAATGTCATTTCTAAAGAATGCAAACTTTCTCTTGCT" //
				+ "ATTTGCTCTATGGTTTTATTACTTTCTTCTATCATTTTCAATCATATTCAACCAAGTTAT" //
				+ "TCAAAAAGCTCAATCCAAATTTTTGTAAAAACAACACCTAATAAGAATGCAATAACGTAC" //
				+ "ATTGCAAGAAATCCTACTAACTCGTCCATAATCAATAATTCCTTATTAGTCTTAATTTGT" //
				+ "AAGCTCTGTATTTTATGGCAATTTATTATTTATTATTATATCCATTCTCTATGA" //
		;

		// Create database & build interval forest
		String genomeName = "test_Campylobacter_fetus_subsp_venerealis_nctc_10354";
		SnpEffectPredictor sep = build(genomeName);
		Gene g = sep.getGene("CFV354_1968");
		Transcript tr = g.subIntervals().iterator().next();
		Assert.assertEquals("Protein sequence differs", prot, tr.protein());
		Assert.assertEquals("CDS sequence differs", cds, tr.cds().toUpperCase());
	}

	@Test
	public void testCase_05_CircularGenome_ExonsOrder() {
		Gpr.debug("Test");

		String expectedProtein = "MGSLEMVPMGAGPPSPGGDPDGYDGGNNSQYPSASGSSGNTPTP" //
				+ "PNDEERESNEEPPPPYEDPYWGNGDRHSDYQPLGTQDQSLYLGLQHDGNDGLPPPPYS" //
				+ "PRDDSSQHIYEEAGRGSMNPVCLPVIVAPYLFWLAAIAASCFTASVSTVVTATGLALS" //
				+ "LLLLAAVASSYAAAQRKLLTPVTVLTAVVTFFAICLTWRIEDPPFNSLLFALLAAAGG" //
				+ "LQGIYVLVMLVLLILAYRRRWRRLTVCGGIMFLACVLVLIVDAVLQLSPLLGAVTVVS" //
				+ "MTLLLLAFVLWLSSPGGLGTLGAALLTLAAALALLASLILGTLNLTTMFLLMLLWTLV" //
				+ "VLLICSSCSSCPLSKILLARLFLYALALLLLASALIAGGSILQTNFKSLSSTEFIPNL" //
				+ "FCMLLLIVAGILFILAILTEWGSGNRTYGPVFMCLGGLLTMVAGAVWLTVMSNTLLSA" //
				+ "WILTAGFLIFLIGFALFGVIRCCRYCCYYCLTLESEERPPTPYRNTV*";

		// Create database & build interval forest
		String genomeName = "testCase";
		String genBankFile = path("Human_herpesvirus_4_uid14413.gbk.gz");
		SnpEffectPredictor sep = buildGeneBank(genomeName, genBankFile, true);
		sep.buildForest();

		// Create variant
		Genome genome = sep.getGenome();
		Gene gene = genome.getGenes().getGeneByName("LMP2");

		// Get transcript
		Transcript tr = gene.get("YP_401631.1");
		Assert.assertTrue("Transcript ID not found", tr != null);

		if (verbose) Gpr.debug("Transcript: " + tr);
		String prot = tr.protein();
		Assert.assertEquals("Protein sequence deas not match", expectedProtein, prot);
	}

	@Test
	public void testCase_06_CircularGenome_ExonsOrder() {
		Gpr.debug("Test");

		String expectedProtein = "MALQTDTQAWRVEIGTRGLMFSNCVPLHLPEGQYHKLRLPVSAY" //
				+ "EALAVARYGLVGSLWEVPAVNSALQCLAAAAPCKDVKIYPSCIFQVHAPMFVTIKTSL" //
				+ "RCLNPHDLCLCLICVGAAILDIPLLCAPRDGAGARAAEGQAAAAQGGKLRVWGRLSPS" //
				+ "SPTSLSLAFPYAGPPPVAWYRHSINLTRSEGVGIGKDCAQDHACPVPPQGHASSAADQ" //
				+ "AGVPERGRKRAHEGPGAGEAASAGRGDVALSQSRALLWRGLGWDTGRGRLAPGLAMSR" //
				+ "DAASGSVHLDIQVDRAEEGWVCDVLLEPGPPTAREGCSLSMDPGLVTLKDAWTLFPLH" //
				+ "PEHDAVVPPKEEIHVMAQGHLQGGTPSLWGFTFQEAACDQWVLRPRVWTAHSPIKMTV" //
				+ "YNCGHKPLHIGPSTRLGLALFWPAERSDNLDAGRIFYQLTSGELYWGRTVARPPTLTL" //
				+ "PVDELRPWPKLTPEEPMQH*" //
		;

		// Create database & build interval forest
		String genomeName = "testCase";
		String genBankFile = path("Human_herpesvirus_4_uid14413.gbk.gz");
		SnpEffectPredictor sep = buildGeneBank(genomeName, genBankFile);
		sep.buildForest();

		// Create variant
		Genome genome = sep.getGenome();
		Gene gene = genome.getGenes().getGeneByName("LF1");
		Transcript tr = gene.iterator().next();
		String prot = tr.protein();

		if (verbose) Gpr.debug("Transcript: " + tr);
		Assert.assertEquals("Protein sequence does not match", expectedProtein, prot);
	}

}