org.snpeff.snpEffect.testCases.unity.TestCasesHgvsIntron 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.Variant;
import org.snpeff.snpEffect.EffectType;
import org.snpeff.snpEffect.VariantEffect;
import org.snpeff.snpEffect.VariantEffects;
import org.snpeff.snpEffect.testCases.integration.TestCasesHgvsBase;
import org.snpeff.util.Gpr;

/**
 * Test random SNP changes
 *
 * @author pcingola
 */
public class TestCasesHgvsIntron extends TestCasesHgvsBase {

	@Test
	public void test_01_intron() {
		Gpr.debug("Test");
		int N = 1000;

		int testIter = -1;
		int testPos = -1;

		// Test N times
		//	- Create a random gene transcript, exons
		//	- Change each base in the exon
		//	- Calculate effect
		for (int checked = 0, it = 1; checked < N; it++) {
			initSnpEffPredictor(true, false);
			boolean tested = false;

			// Skip test?
			if (testIter >= 0 && it < testIter) {
				Gpr.debug("Skipping iteration: " + it);
				continue;
			}

			// No introns? Nothing to test
			if (transcript.introns().size() < 1) continue;

			// Character representation
			String trstr = transcript.toStringAsciiArt(false);
			char bases[] = trstr.toCharArray();

			// Show data
			if (verbose) {
				System.out.println("HGSV Intron\titeration:" + checked + "\t" + (transcript.isStrandPlus() ? "+" : "-"));
				System.out.println(trstr);
				System.out.println("Length   : " + transcript.size());
				System.out.println("CDS start: " + transcript.getCdsStart());
				System.out.println("CDS end  : " + transcript.getCdsEnd());
				System.out.println(transcript);
			} else Gpr.showMark(it, 1);

			// Check each intronic base
			for (int j = 0, pos = transcript.getStart(); pos < transcript.getEnd(); j++, pos++) {
				// Intron?
				if (bases[j] == '-') {
					tested = true;

					// Skip base?
					if (testPos >= 0 && pos < testPos) {
						Gpr.debug("\tSkipping\tpos: " + pos + " [" + j + "]");
						continue;
					}

					// Ref & Alt
					String refStr = "A", altStr = "T";

					// Calculate expected hgsv string
					String hgsv = intronHgsv(bases, j, pos, refStr, altStr);

					// Calculate effect and compare to expected
					Variant sc = new Variant(transcript.getChromosome(), pos, refStr, altStr, "");
					VariantEffects ceffs = snpEffectPredictor.variantEffect(sc);
					VariantEffect ceff = ceffs.get();
					String hgsvEff = ceffs.get().getHgvs();
					if (debug) System.out.println("\tpos: " + pos + " [" + j + "]\thgsv: '" + hgsv + "'\tEff: '" + hgsvEff + "'\t" + ceff.getEffectType());

					// Is this an intron? (i.e. skip other effects, such as splice site)
					// Compare expected to real HGSV strings
					if (ceff.getEffectType() == EffectType.INTRON) Assert.assertEquals(hgsv, hgsvEff);
				}
			}

			if (tested) checked++;
		}
		System.err.println("");
	}

}