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

Go to download

Show more of this group Show more artifacts with this name
Show all versions of SnpEff Show documentation

Variant annotation and effect prediction package.

The newest version!

package org.snpeff.snpEffect.testCases.integration;

import java.util.List;

import org.junit.Assert;
import org.junit.Test;
import org.snpeff.SnpEff;
import org.snpeff.snpEffect.commandLine.SnpEffCmdEff;
import org.snpeff.util.Gpr;
import org.snpeff.vcf.VcfEffect;
import org.snpeff.vcf.VcfEntry;

/**
 * Test random SNP changes
 *
 * @author pcingola
 */
public class TestCasesIntegrationMnp extends TestCasesIntegrationBase {

	@Test
	public void test_01() {
		Gpr.debug("Test");
		// Run
		String args[] = { "-classic", "-noHgvs", "-ud", "0", "testHg3766Chr1", path("test.mnp.01.vcf") };
		SnpEff cmd = new SnpEff(args);
		SnpEffCmdEff snpeff = (SnpEffCmdEff) cmd.cmd();
		snpeff.setVerbose(verbose);
		snpeff.setSupressOutput(!verbose);
		snpeff.setDebug(debug);
		List results = snpeff.run(true);

		// Check
		Assert.assertEquals(1, results.size());
		VcfEntry result = results.get(0);

		for (VcfEffect eff : result.getVcfEffects()) {
			String aa = eff.getAa();
			String aaNumStr = aa.substring(1, aa.length() - 1);
			int aanum = Gpr.parseIntSafe(aaNumStr);
			if (verbose) System.out.println("AA: '" + eff.getAa() + "'\tAA Num Str: '" + aaNumStr + "'\teff: " + eff);

			if (aanum <= 0) throw new RuntimeException("Missing AA number!");
		}
	}

}