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

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Variant annotation and effect prediction package.

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package org.snpeff.snpEffect.testCases.integration;

import org.junit.Test;
import org.snpeff.SnpEff;
import org.snpeff.snpEffect.commandLine.SnpEffCmdBuild;
import org.snpeff.snpEffect.commandLine.SnpEffCmdProtein;
import org.snpeff.util.Gpr;

import junit.framework.Assert;

/**
 * Test case for EMBL file parsing (database creation)
 *
 * @author pcingola
 */
public class TestCasesIntegrationGenBank extends TestCasesIntegrationBase {

	int exonToStringVersionOri;

	public TestCasesIntegrationGenBank() {
		super();
	}

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

		// Build genome
		String genome = "test_NC_031965.1";
		String args[] = { "build", genome };
		SnpEff snpeff = new SnpEff(args);
		snpeff.setVerbose(verbose);
		snpeff.setDebug(debug);
		SnpEffCmdBuild snpeffBuild = (SnpEffCmdBuild) snpeff.cmd();
		snpeffBuild.run();

		// Check
		SnpEffCmdProtein sprot = snpeffBuild.getSnpEffCmdProtein();
		Assert.assertEquals("Wrong number of matching proteins", 3, sprot.getTotalOk());
		Assert.assertEquals("Errors while checking sequenced", 0, sprot.getTotalErrors());
	}
}