org.snpeff.snpEffect.testCases.unity.TestCasesNmers Maven / Gradle / Ivy

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package org.snpeff.snpEffect.testCases.unity;

import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.util.ArrayList;
import java.util.Random;

import org.junit.Test;
import org.snpeff.binseq.coder.DnaCoder;
import org.snpeff.nmer.Nmer;
import org.snpeff.util.Gpr;

public class TestCasesNmers {

	public static boolean verbose = false;

	/**
	 * Create a random sequence of length 'len'
	 * @param len
	 * @param rand
	 * @return
	 */
	String randSeq(int len, Random rand) {
		StringBuilder sb = new StringBuilder();
		// Create a random sequence
		for (int i = 0; i < len; i++) {
			int r = rand.nextInt() & 0x03;
			sb.append(DnaCoder.get().toBase(r));
		}
		return sb.toString();
	}

	@Test
	public void test_03_Nmers() {
		Gpr.debug("Test");
		long seed = 20100615;
		Random rand = new Random(seed);

		int numTests = 100;

		// Test all lengths
		for (int len = 1; len <= 32; len++) {
			for (int t = 0; t < numTests; t++) {
				String seq = randSeq(len, rand); // Create a random sequence
				if (verbose) System.out.println("Nmer test:" + t + "\tlen:" + len + "\t" + seq);
				Nmer nmer = new Nmer(seq);
				if (!seq.equals(nmer.toString())) throw new RuntimeException("Sequences do not match:\n\tSeq    :\t" + seq + "\n\tBinSeq :\t" + nmer);
			}
		}
	}

	@Test
	public void test_20_Nmers_read_write() {
		Gpr.debug("Test");
		String testFile = "/tmp/nmer_test.bin";
		int nmerSize = 32;
		int numNmers = 100000;
		try {
			// Initialize
			FileOutputStream os = new FileOutputStream(new File(testFile));
			Random rand = new Random(20100825);
			ArrayList list = new ArrayList();

			// Create Nmers and write them to file
			for (int i = 0; i < numNmers; i++) {
				Nmer nmer = new Nmer(nmerSize);
				nmer.setNmer(rand.nextLong());
				list.add(nmer);
				nmer.write(os);
			}
			os.close();

			// Read nmers from file and compare to originals
			Nmer nmer = new Nmer(nmerSize);
			FileInputStream is = new FileInputStream(new File(testFile));
			for (int i = 0; nmer.read(is) >= 0; i++) {
				Nmer nmerOri = list.get(i);
				if (nmerOri.getNmer() != nmer.getNmer()) throw new RuntimeException("Nmers differ:\n\t" + nmerOri + "\t" + Long.toHexString(nmerOri.getNmer()) + "\n\t" + nmer + "\t" + Long.toHexString(nmer.getNmer()));
			}
			is.close();
		} catch (Exception e) {
			throw new RuntimeException(e);
		}
	}

}