org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationGenomicSequences Maven / Gradle / Ivy

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package org.snpeff.snpEffect.testCases.integration;

import junit.framework.Assert;

import org.junit.Test;
import org.snpeff.binseq.GenomicSequences;
import org.snpeff.interval.Exon;
import org.snpeff.interval.Gene;
import org.snpeff.interval.Transcript;
import org.snpeff.snpEffect.commandLine.SnpEffCmdEff;
import org.snpeff.util.Gpr;

/**
 *
 * Test case for genomic sequences
 */
public class TestCasesIntegrationGenomicSequences {

	boolean debug = false;
	boolean verbose = false || debug;

	public TestCasesIntegrationGenomicSequences() {
		super();
	}

	/**
	 * Check that we can recover sequences from all exons using GneomicSequence class
	 */
	@Test
	public void test_01() {
		Gpr.debug("Test");
		String genome = "testHg3775Chr1";

		// Create SnpEff
		String args[] = { genome };
		SnpEffCmdEff snpeff = new SnpEffCmdEff();
		snpeff.parseArgs(args);
		snpeff.setDebug(debug);
		snpeff.setVerbose(verbose);
		snpeff.setSupressOutput(!verbose);

		// Load genome
		snpeff.load();

		GenomicSequences genomicSequences = snpeff.getConfig().getGenome().getGenomicSequences();
		int i = 1;
		for (Gene g : snpeff.getConfig().getGenome().getGenes()) {
			for (Transcript tr : g) {
				for (Exon ex : tr) {
					Gpr.showMark(i++, 100);

					String seq = genomicSequences.querySequence(ex);
					if (verbose) System.out.println(g.getGeneName() + "\t" + tr.getId() + "\t" + ex.getId() + "\n\t" + ex.getSequence() + "\n\t" + seq);

					// Sanity checks
					Assert.assertNotNull(seq == null);
					Assert.assertEquals(seq, ex.getSequence());
				}
			}
		}

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

	/**
	 * Check that we can recover sequences from all exons using GenomicSequences
	 * class, WITHOUT loading sequence form databases
	 */
	@Test
	public void test_02() {
		Gpr.debug("Test");
		String genome = "testHg3775Chr22";

		// Create SnpEff
		String args[] = { genome };
		SnpEffCmdEff snpeff = new SnpEffCmdEff();
		snpeff.parseArgs(args);
		snpeff.setDebug(debug);
		snpeff.setVerbose(verbose);
		snpeff.setSupressOutput(!verbose);

		// Load genome
		snpeff.load();

		// Disable loading
		GenomicSequences genomicSequences = snpeff.getConfig().getGenome().getGenomicSequences();
		genomicSequences.setDisableLoad(true);

		int i = 1;
		for (Gene g : snpeff.getConfig().getGenome().getGenes()) {
			for (Transcript tr : g) {
				for (Exon ex : tr) {
					Gpr.showMark(i++, 100);
					String seq = genomicSequences.querySequence(ex);
					if (verbose) System.out.println(g.getGeneName() + "\t" + tr.getId() + "\t" + ex.getId() + "\n\t" + ex.getSequence() + "\n\t" + seq);

					// Sanity checks
					Assert.assertNotNull(seq == null);
					Assert.assertEquals(seq, ex.getSequence());
				}
			}
		}

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

}