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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.VariantEffect;
import org.snpeff.snpEffect.VariantEffects;
import org.snpeff.snpEffect.testCases.integration.TestCasesHgvsBase;
import org.snpeff.util.Gpr;
import org.snpeff.util.GprSeq;
import org.snpeff.vcf.VcfEntry;

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

	@Test
	public void test_01_coding() {
		Gpr.debug("Test");

		int N = 1000;
		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(false, true);
			if (debug) System.out.println("HGSV Test iteration: " + i + "\n" + transcript);
			else if (verbose) System.out.println("HGSV Coding\titeration: " + i + "\t" + (transcript.isStrandPlus() ? "+" : "-") + "\t" + transcript.cds());
			else Gpr.showMark(i + 1, 1);

			int cdsBaseNum = 0;

			// For each exon...
			for (Exon exon : transcript.sortedStrand()) {
				// For each base in this exon...
				for (int pos = exon.getStart(); (exon.getStart() <= pos) && (pos <= exon.getEnd()); pos++, 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.aaThreeLetterCode(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.aaThreeLetterCode(codonTable.aa(newCodon));
						String protHgvs = "";
						String dnaHgvs = "c." + (cdsBaseNum + 1) + refBase + ">" + snp;

						// Effect
						if (newAa.equals(aa)) {
							if ((cdsCodonNum == 0) && (codonTable.isStart(codon))) {
								if (codonTable.isStart(newCodon)) protHgvs = "p." + aa + "1?";
								else protHgvs = "p." + aa + "1?";
							} else protHgvs = "p." + aa + (cdsCodonNum + 1) + newAa;
						} else {
							if ((cdsCodonNum == 0) && (codonTable.isStart(codon))) {
								if (codonTable.isStart(newCodon)) protHgvs = "p." + aa + "1?";
								else protHgvs = "p." + aa + "1?";
							} else if (codonTable.isStop(codon)) protHgvs = "p." + aa + (cdsCodonNum + 1) + newAa + "ext*?";
							else if (codonTable.isStop(newCodon)) protHgvs = "p." + aa + (cdsCodonNum + 1) + "*";
							else protHgvs = "p." + aa + (cdsCodonNum + 1) + newAa;
						}

						String effectExpected = protHgvs + "/" + dnaHgvs;

						// Create a SeqChange
						Variant variant = new Variant(chromosome, pos, refBase + "", snp + "", "");

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

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

						// There should be only one effect
						Assert.assertEquals(true, effects.size() <= 1);

						// Show
						if (effects.size() == 1) {
							VariantEffect effect = effects.get();
							String effStr = effect.getHgvs();

							if (debug) System.out.println("\tPos: " + pos //
									+ "\tCDS base num: " + cdsBaseNum + " [" + cdsCodonNum + ":" + cdsCodonPos + "]" //
									+ "\t" + variant //
									+ "\tCodon: " + codon + " -> " + newCodon //
									+ "\tAA: " + aa + " -> " + newAa //
									+ "\tEffect expected: " + effectExpected //
									+ "\tEffect: " + effStr);

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

							// Check that effect can be inserted into a VCF field
							if (!VcfEntry.isValidInfoValue(effStr)) {
								String err = "No white-space, semi-colons, or equals-signs are permitted in INFO field. Value:\"" + effStr + "\"";
								System.err.println(err);
								throw new RuntimeException(err);
							}

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

}