org.snpeff.snpEffect.testCases.unity.TestCasesSnps 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.codons.CodonTable;
import org.snpeff.interval.Exon;
import org.snpeff.interval.Variant;
import org.snpeff.snpEffect.VariantEffect;
import org.snpeff.snpEffect.VariantEffects;
import org.snpeff.util.Gpr;
import org.snpeff.util.GprSeq;

import junit.framework.Assert;

/**
 * Test random SNP changes
 *
 * @author pcingola
 */
public class TestCasesSnps extends TestCasesBase {

	public static int N = 1000;

	public TestCasesSnps() {
		super();
	}

	String effectStr(VariantEffect effect) {
		String effStr = effect.effect(true, true, true, false, false);
		String aaStr = effect.getAaChangeOld();
		int idx = effStr.indexOf('(');
		return effStr.substring(0, idx) + "(" + aaStr + ")";
	}

	@Override
	protected void init() {
		super.init();
		randSeed = 20100629;
	}

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

		CodonTable codonTable = genome.codonTable();

		// Test N times
		//	- Create a random gene transcript, exons
		//	- Change each base in the exon
		//	- Calculate effect
		for (int i = 0; i < N; i++) {
			initSnpEffPredictor();
			if (debug) System.out.println("SNP Test iteration: " + i + "\n" + transcript);
			else if (verbose) System.out.println("SNP Test iteration: " + i + "\t" + transcript.getStrand() + "\t" + transcript.cds());
			else Gpr.showMark(i + 1, 1);

			int cdsBaseNum = 0;

			// For each exon...
			for (Exon exon : transcript.sortedStrand()) {
				int step = exon.isStrandPlus() ? 1 : -1;
				int beg = exon.isStrandPlus() ? exon.getStart() : exon.getEnd();

				// For each base in this exon...
				for (int pos = beg; (pos >= exon.getStart()) && (pos <= exon.getEnd()); pos += step, cdsBaseNum++) {
					// Reference base
					char refBase = chromoBases[pos]; // exon.basesAt(pos - exon.getStart(), 1).charAt(0);
					refBase = Character.toUpperCase(refBase);
					// Codon number
					int cdsCodonNum = cdsBaseNum / 3;
					int cdsCodonPos = cdsBaseNum % 3;

					int minCodonPos = cdsCodonNum * 3;
					int maxCodonPos = minCodonPos + 3;
					if (maxCodonPos < transcript.cds().length()) {
						String codon = transcript.cds().substring(minCodonPos, maxCodonPos);
						codon = codon.toUpperCase();
						String aa = codonTable.aa(codon);

						// Get a random base different from 'refBase'
						char snp = refBase;
						while (snp == refBase) {
							snp = Character.toUpperCase(GprSeq.randBase(rand));
						}

						// Codon change
						String newCodon = codon.substring(0, cdsCodonPos) + snp + codon.substring(cdsCodonPos + 1);
						String newAa = codonTable.aa(newCodon);
						String effectExpected = "";

						// Effect
						if (newAa.equals(aa)) {
							if ((cdsCodonNum == 0) && (codonTable.isStart(codon))) {
								if (codonTable.isStart(newCodon)) effectExpected = "SYNONYMOUS_START(" + aa + ")";
								else effectExpected = "START_LOST(" + aa + ")";
							} else if (aa.equals("*")) effectExpected = "SYNONYMOUS_STOP(" + aa + ")";
							else effectExpected = "SYNONYMOUS_CODING(" + aa + ")";
						} else {
							if ((cdsCodonNum == 0) && (codonTable.isStart(codon))) {
								if (codonTable.isStart(newCodon)) effectExpected = "NON_SYNONYMOUS_START(" + aa + "/" + newAa + ")";
								else effectExpected = "START_LOST(" + aa + "/" + newAa + ")";
							} else if (codonTable.isStop(codon)) effectExpected = "STOP_LOST(" + aa + "/" + newAa + ")";
							else if (codonTable.isStop(newCodon)) effectExpected = "STOP_GAINED(" + aa + "/" + newAa + ")";
							else effectExpected = "NON_SYNONYMOUS_CODING(" + aa + "/" + newAa + ")";
						}

						// Create a variant
						if (exon.isStrandMinus()) {
							snp = GprSeq.wc(snp);
							refBase = GprSeq.wc(refBase);
						}
						Variant variant = new Variant(chromosome, pos, refBase + "", snp + "", "");

						if (!variant.isVariant()) effectExpected = "EXON";

						// Calculate effects
						VariantEffects effects = snpEffectPredictor.variantEffect(variant);

						// Checknumber of results
						Assert.assertEquals(true, effects.size() == 1);
						if (debug) System.out.println(effects);

						// Check effect
						VariantEffect effect = effects.get();
						String effStr = effectStr(effect);
						if (debug) System.out.println("\tPos: " + pos //
								+ "\tCDS base num: " + cdsBaseNum + " [" + cdsCodonNum + ":" + cdsCodonPos + "]" //
								+ "\t" + variant //
								+ "\tCodon: " + codon + " -> " + newCodon //
								+ "\tAA: " + aa + " -> " + newAa //
								+ "\tEffect: " + effStr);

						// Check effect
						Assert.assertEquals(effectExpected, effStr);
					}
				}
			}
		}

		System.err.println("");
	}

}