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

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

	public static int N = 1000;

	public TestCasesIns() {
		init();
	}

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

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

		// Test N times
		//	- Create a random gene transcript, exons
		//	- Create a random Insert at each position
		//	- Calculate effect
		for (int i = 0; i < N; i++) {
			initSnpEffPredictor();
			CodonTable codonTable = genome.codonTable();
			if (debug) System.out.println("INS Test iteration: " + i + "\n" + transcript);
			else if (verbose) System.out.println("INS Test iteration: " + i + "\t" + (transcript.isStrandPlus() ? "+" : "-") + "\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++) {

					// Get a random base different from 'refBase'
					int insLen = rand.nextInt(10) + 1;
					String insPlus = GprSeq.randSequence(rand, insLen); // Insertion (plus strand)
					String ins = insPlus;

					// Codon number
					int cdsCodonNum = cdsBaseNum / 3;
					int cdsCodonPos = cdsBaseNum % 3;

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

						// Codon change
						String codonNew = "", aaNew = "";

						// Create a SeqChange
						if (exon.isStrandMinus()) ins = GprSeq.reverseWc(insPlus);
						Variant variant = new Variant(chromosome, pos, "", "+" + ins, "");

						// Is it an insertion?
						Assert.assertEquals(true, variant.isIns());

						// Codon change
						int idx = cdsCodonPos;
						if (transcript.isStrandMinus()) idx++; // Insert AFTER base (in negative strand)
						codonNew = codonOld.substring(0, idx) + insPlus + codonOld.substring(idx);
						aaNew = codonTable.aa(codonNew);

						// Expected Effect
						EffectType effectExpected = null;
						String aaExpected = "";
						if (insLen % 3 != 0) {
							effectExpected = EffectType.FRAME_SHIFT;
							aaExpected = aaOld + "/" + aaNew;
						} else {
							if (cdsCodonPos == 0) {
								effectExpected = EffectType.CODON_INSERTION;
								aaExpected = aaOld + "/" + aaNew;
							} else {
								if (codonNew.startsWith(codonOld)) {
									effectExpected = EffectType.CODON_INSERTION;
									aaExpected = aaOld + "/" + aaNew;
								} else {
									effectExpected = EffectType.CODON_CHANGE_PLUS_CODON_INSERTION;
									aaExpected = aaOld + "/" + aaNew;
								}
							}

							if ((cdsCodonNum == 0) && codonTable.isStartFirst(codonOld) && !codonTable.isStartFirst(codonNew)) {
								effectExpected = EffectType.START_LOST;
								aaExpected = aaOld + "/" + aaNew;
							} else if ((aaOld.indexOf('*') >= 0) && (aaNew.indexOf('*') < 0)) {
								effectExpected = EffectType.STOP_LOST;
								aaExpected = aaOld + "/" + aaNew;
							} else if ((aaNew.indexOf('*') >= 0) && (aaOld.indexOf('*') < 0)) {
								effectExpected = EffectType.STOP_GAINED;
								aaExpected = aaOld + "/" + aaNew;
							}
						}

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

						// There should be at least one effect
						Assert.assertTrue(effects.size() > 0);

						// Show
						boolean ok = false;
						for (VariantEffect effect : effects) {
							String effFullStr = effect.effect(true, true, false, false, false);
							String effStr = effect.effect(true, false, false, false, false);
							String aaStr = effect.getAaChangeOld();

							if (debug) System.out.println("\tPos: " + pos //
									+ "\tCDS base num: " + cdsBaseNum + " [" + cdsCodonNum + ":" + cdsCodonPos + "]" //
									+ "\t" + variant //
									+ "\tCodon: " + codonOld + " -> " + codonNew //
									+ "\tAA: " + aaOld + " -> " + aaNew //
									+ "\n\t\tEffect          : '" + effStr + "'\t'" + effFullStr + "'" //
									+ "\n\t\tEffect expected : '" + effectExpected + "'" //
									+ "\n\t\tAA              : '" + aaStr + "'" //
									+ "\n\t\tAA expected     : '" + aaExpected + "'" //
							);

							// Check that there is a match
							ok |= effect.hasEffectType(effectExpected);
						}

						// Check effect
						Assert.assertTrue("Could not find effect '" + effectExpected + "' and AA '" + aaExpected + "'", ok);
					}
				}
			}
		}

		System.err.println("");
	}
}