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

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package org.snpeff.snpEffect.testCases.unity;

import java.util.HashSet;
import java.util.Map;
import java.util.Random;

import org.junit.Test;
import org.snpeff.interval.Chromosome;
import org.snpeff.interval.Genome;
import org.snpeff.interval.Marker;
import org.snpeff.interval.MarkerUtil;
import org.snpeff.interval.Markers;
import org.snpeff.util.Gpr;
import org.snpeff.util.Tuple;

public class TestCasesMarkerUtils {

	int maxLen = 100;
	int minLen = 1;
	int maxGap = 100;
	int minGap = 50;
	boolean verbose = false;
	boolean compareCdsTestsEnable = false;
	Random rand;
	Genome genome;

	public TestCasesMarkerUtils() {
		super();
		initRand();
		String genomeName = "testCaseHg";
		genome = new Genome(genomeName);

		// Create chromosomes
		for (int i = 1; i < 22; i++)
			genome.add(new Chromosome(genome, 0, 0, "" + i));
		genome.add(new Chromosome(genome, 0, 0, "X"));
		genome.add(new Chromosome(genome, 0, 0, "Y"));
	}

	/**
	 * Create a list of markers
	 * @param chr
	 * @param numMarkers
	 * 
	 * @return Two collections of markers (in a tuple), the original one and the collapsed one
	 */
	Tuple createMarkers(Chromosome chr, int numMarkers) {
		Markers markers = new Markers();
		Markers markersCollapsed = new Markers();
		int start = 0, startPrev = -1, end = 0, gap = 0;

		Marker m = null, mcol = null;
		for (int i = 0; i < numMarkers; i++) {
			// Interval size
			int size = rand.nextInt(maxLen) + minLen;
			end = start + size;
			if (startPrev < 0) startPrev = start;

			// Create marker
			m = new Marker(chr, start, end, false, "");
			markers.add(m);

			// Next interval
			gap = rand.nextInt(maxGap);
			mcol = new Marker(chr, startPrev, end, false, "");
			if (gap <= minGap) {
				gap = 1;
			} else {
				markersCollapsed.add(mcol);
				mcol = null;
				startPrev = -1;
			}

			start = end + gap;
		}
		if (mcol != null) markersCollapsed.add(mcol);

		return new Tuple(markers, markersCollapsed);
	}

	void initRand() {
		rand = new Random(20121115);
	}

	/**
	 * Show a collection of sorted intervals as a string
	 * @param markers
	 * @return
	 */
	String markers2string(Markers markers) {
		StringBuilder sb = new StringBuilder();

		int prevEnd = -1;
		markers.sort(false, false);
		for (Marker m : markers) {
			if (prevEnd >= 0) {
				for (int i = prevEnd; i < m.getStart(); i++)
					sb.append('-');
			}

			for (int i = m.getStart(); i <= m.getEnd(); i++)
				sb.append('M');

			prevEnd = m.getEnd() + 1;
		}

		return sb.toString();
	}

	/**
	 * Test for collapsing markers with zero gaps 
	 */
	@Test
	public void test_collapseZeroGap() {
		Gpr.debug("Test");
		initRand();
		int numMarkers = 20;
		Chromosome chr = genome.getChromosome("1");

		for (int num = 1; num < 1000; num++) {
			// Create markers
			Tuple tupleMarkers = createMarkers(chr, numMarkers);
			Markers markersOri = tupleMarkers.first;
			Markers markersCollapsedOri = tupleMarkers.second;

			//---
			// Compare created markers
			//---
			String mStr = markers2string(markersOri);
			String mColOriStr = markers2string(markersCollapsedOri);
			if (verbose) Gpr.debug("Iteration : " + num + "\n\tMarkers           : " + mStr + "\n\tMarkers collapsed : " + mColOriStr);

			// Are generated intervasl OK?
			if (!mStr.equals(mColOriStr)) {
				System.err.println("Markers : ");
				for (Marker m : markersOri)
					System.err.println(m);

				System.err.println("Markers collapsed: ");
				for (Marker m : markersCollapsedOri)
					System.err.println(m);

				throw new RuntimeException("Error creating markers! Markers and collapsed marker do not match!\n\t" + mStr + "\n\t" + mColOriStr);
			}

			//---
			// Compare to Markers.collapseZeroGap
			//---

			// Collapse
			Map collapse = MarkerUtil.collapseZeroGap(markersOri);
			// Get unique markers
			HashSet collapsed = new HashSet();
			collapsed.addAll(collapse.values());

			Markers markers = new Markers();
			markers.addAll(collapsed);
			String mColStr = markers2string(markers); // Create string 

			// Are generated intervasl OK?
			if (!mColStr.equals(mStr)) {
				Gpr.debug("Error checing markers! Markers and collapsed marker do not match!\n\t" + mStr + "\n\t" + mColStr);

				System.err.println("Markers : ");
				for (Marker m : markersOri)
					System.err.println(m);

				System.err.println("Markers collapsed: ");
				markers = new Markers();
				markers.addAll(collapse.keySet());
				Markers keySorted = markers.sort(false, false);
				for (Marker mkey : keySorted)
					System.err.println(mkey + "\t->\t" + collapse.get(mkey));

				throw new RuntimeException("Error checing markers! Markers and collapsed marker do not match!\n\t" + mStr + "\n\t" + mColStr);
			}
		}
	}
}