org.snpeff.snpEffect.testCases.unity.TestCasesApplyIns 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.Test;
import org.snpeff.interval.Variant;
import org.snpeff.util.Gpr;

/**
 * Test cases: apply a variant (INS) to a transcript
 *
 */
public class TestCasesApplyIns extends TestCasesBaseApply {

	public TestCasesApplyIns() {
		super();
	}

	/**
	 * Variant before exon
	 */
	@Test
	public void test_apply_variant_01() {
		Gpr.debug("Test");

		Variant variant = new Variant(transcript.getParent(), 290, "", "ACG");
		checkApplyIns(variant, transcript.cds(), transcript.protein(), 1, 303, 402);
	}

	/**
	 * Variant before exon
	 */
	@Test
	public void test_apply_variant_02() {
		Gpr.debug("Test");

		Variant variant = new Variant(transcript.getParent(), 297, "", "ACG");
		checkApplyIns(variant, transcript.cds(), transcript.protein(), 1, 303, 402);
	}

	/**
	 * Variant overlapping exon start
	 */
	@Test
	public void test_apply_variant_03() {
		Gpr.debug("Test");

		Variant variant = new Variant(transcript.getParent(), 299, "", "ACG");
		checkApplyIns(variant, transcript.cds(), transcript.protein(), 1, 303, 402);
	}

	/**
	 * Variant at exon start
	 */
	@Test
	public void test_apply_variant_04() {
		Gpr.debug("Test");

		Variant variant = new Variant(transcript.getParent(), 300, "", "ACG");

		String expectedCds = "atgtccgcaggtgaaggcatacacgctgcgcgtatactgatgttacctcgatggattttgtcagaaatatggtgcccaggacgcgaagggcatattatgg" // Exon[0]
				+ "ACGtgtttgggaattcacgggcacggttctgcagcaagctgaattggcagctcggcataaatcccgaccccatcgtcacgcacggatcaattcatcctcaacg".toLowerCase() // Exon[1]
				+ "ggtagaggaaaagcacctaacccccattgagcaggatctctttcgtaatactctgtatcgattaccgatttatttgattccccacatttatttcatcggg" // Exon[2]
				;

		checkApplyIns(variant, expectedCds, null, 1, 300, 402);

	}

	/**
	 * Variant in exon
	 */
	@Test
	public void test_apply_variant_05() {
		Gpr.debug("Test");

		Variant variant = new Variant(transcript.getParent(), 310, "", "ACG");

		String expectedCds = "atgtccgcaggtgaaggcatacacgctgcgcgtatactgatgttacctcgatggattttgtcagaaatatggtgcccaggacgcgaagggcatattatgg" // Exon[0]
				+ "tgtttgggaaACGttcacgggcacggttctgcagcaagctgaattggcagctcggcataaatcccgaccccatcgtcacgcacggatcaattcatcctcaacg".toLowerCase() // Exon[1]
				+ "ggtagaggaaaagcacctaacccccattgagcaggatctctttcgtaatactctgtatcgattaccgatttatttgattccccacatttatttcatcggg" // Exon[2]
				;

		checkApplyIns(variant, expectedCds, null, 1, 300, 402);

	}

	/**
	 * Variant in exon
	 */
	@Test
	public void test_apply_variant_06() {
		Gpr.debug("Test");

		Variant variant = new Variant(transcript.getParent(), 399, "", "ACG");

		String expectedCds = "atgtccgcaggtgaaggcatacacgctgcgcgtatactgatgttacctcgatggattttgtcagaaatatggtgcccaggacgcgaagggcatattatgg" // Exon[0]
				+ "tgtttgggaattcacgggcacggttctgcagcaagctgaattggcagctcggcataaatcccgaccccatcgtcacgcacggatcaattcatcctcaacACGg".toLowerCase() // Exon[1]
				+ "ggtagaggaaaagcacctaacccccattgagcaggatctctttcgtaatactctgtatcgattaccgatttatttgattccccacatttatttcatcggg" // Exon[2]
				;

		checkApplyIns(variant, expectedCds, null, 1, 300, 402);

	}

	/**
	 * Variant overlapping exon end
	 */
	@Test
	public void test_apply_variant_07() {
		Gpr.debug("Test");

		Variant variant = new Variant(transcript.getParent(), 399, "", "ACG");

		String expectedCds = "atgtccgcaggtgaaggcatacacgctgcgcgtatactgatgttacctcgatggattttgtcagaaatatggtgcccaggacgcgaagggcatattatgg" // Exon[0]
				+ "tgtttgggaattcacgggcacggttctgcagcaagctgaattggcagctcggcataaatcccgaccccatcgtcacgcacggatcaattcatcctcaacACGg".toLowerCase() // Exon[1]
				+ "ggtagaggaaaagcacctaacccccattgagcaggatctctttcgtaatactctgtatcgattaccgatttatttgattccccacatttatttcatcggg" // Exon[2]
				;

		checkApplyIns(variant, expectedCds, null, 1, 300, 402);

	}

	/**
	 * Variant right after exon end
	 */
	@Test
	public void test_apply_variant_08() {
		Gpr.debug("Test");

		Variant variant = new Variant(transcript.getParent(), 400, "", "ACG");
		checkApplyIns(variant, transcript.cds(), transcript.protein(), 1, 300, 399);
	}

	/**
	 * Variant after exon end
	 */
	@Test
	public void test_apply_variant_09() {
		Gpr.debug("Test");

		Variant variant = new Variant(transcript.getParent(), 410, "", "ACG");
		checkApplyIns(variant, transcript.cds(), transcript.protein(), 1, 300, 399);
	}

	/**
	 * Variant over exon: variant is larger than exon, starts before exon and overlaps the whole exon
	 */
	@Test
	public void test_apply_variant_10() {
		Gpr.debug("Test");

		Variant variant = new Variant(transcript.getParent(), 290, "", "ATTGGCTCGACGCTCATTCACTCCAACAGCCCGGGACCCCCGCTCAATTATTTCACTCACCGGGAAAATTGTACCGATTGTCCGTGCCTTACTTCAAATGACATCCGCAGGTGAAGGCAT");
		checkApplyIns(variant, transcript.cds(), transcript.protein(), 1, 420, 519);
	}

	/**
	 * Variant over exon: variant is larger than exon and starts right at exons start and ends after exon end
	 */
	@Test
	public void test_apply_variant_11() {
		Gpr.debug("Test");

		String seq = "ATTGGCTCGACGCTCATTCACTCCAACAGCCCGGGACCCCCGCTCAATTATTTCACTCACCGGGAAAATTGTACCGATTGTCCGTGCCTTACTTCAAATGACATCCGCAGGTGAAGGCAT";
		Variant variant = new Variant(transcript.getParent(), 300, "", seq);

		String expectedCds = "atgtccgcaggtgaaggcatacacgctgcgcgtatactgatgttacctcgatggattttgtcagaaatatggtgcccaggacgcgaagggcatattatgg" // Exon[0]
				+ seq.toLowerCase() + "tgtttgggaattcacgggcacggttctgcagcaagctgaattggcagctcggcataaatcccgaccccatcgtcacgcacggatcaattcatcctcaacg" // Exon[1]
				+ "ggtagaggaaaagcacctaacccccattgagcaggatctctttcgtaatactctgtatcgattaccgatttatttgattccccacatttatttcatcggg" // Exon[2]
				;

		checkApplyIns(variant, expectedCds, null, 1, 300, 519);

	}

	/**
	 * Variant over exon: variant is larger than exon, starts before exon start and end right at exon end
	 */
	@Test
	public void test_apply_variant_12() {
		Gpr.debug("Test");

		String seq = "ATTGGCTCGACGCTCATTCACTCCAACAGCCCGGGACCCCCGCTCAATTATTTCACTCACCGGGAAAATTGTACCGATTGTCCGTGCCTTACTTCAAATGACATCCGCAG";
		Variant variant = new Variant(transcript.getParent(), 290, "", seq);

		checkApplyIns(variant, transcript.cds(), transcript.protein(), 1, 410, 509);

	}

	/**
	 * Variant over exon: variant is on the same coordiantes as exon
	 */
	@Test
	public void test_apply_variant_13() {
		Gpr.debug("Test");

		String seq = "ATTGGCTCGACGCTCATTCACTCCAACAGCCCGGGACCCCCGCTCAATTATTTCACTCACCGGGAAAATTGTACCGATTGTCCGTGCCTTACTTCAAATG";
		Variant variant = new Variant(transcript.getParent(), 300, "", seq);

		String expectedCds = "atgtccgcaggtgaaggcatacacgctgcgcgtatactgatgttacctcgatggattttgtcagaaatatggtgcccaggacgcgaagggcatattatgg" // Exon[0]
				+ seq.toLowerCase() + "tgtttgggaattcacgggcacggttctgcagcaagctgaattggcagctcggcataaatcccgaccccatcgtcacgcacggatcaattcatcctcaacg" // Exon[1]
				+ "ggtagaggaaaagcacctaacccccattgagcaggatctctttcgtaatactctgtatcgattaccgatttatttgattccccacatttatttcatcggg" // Exon[2]
				;

		checkApplyIns(variant, expectedCds, null, 1, 300, 499);
	}

}