69 lines
4.1 KiB
Java
Executable File
69 lines
4.1 KiB
Java
Executable File
package org.broadinstitute.sting.utils;
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import org.testng.Assert;
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import org.broadinstitute.sting.BaseTest;
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import org.testng.annotations.Test;
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import org.testng.annotations.BeforeClass;
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public class BaseUtilsUnitTest extends BaseTest {
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@BeforeClass
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public void init() { }
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@Test
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public void testMostFrequentBaseFraction() {
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logger.warn("Executing testMostFrequentBaseFraction");
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compareFrequentBaseFractionToExpected("AAAAA", 1.0);
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compareFrequentBaseFractionToExpected("ACCG", 0.5);
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compareFrequentBaseFractionToExpected("ACCCCTTTTG", 4.0/10.0);
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}
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private void compareFrequentBaseFractionToExpected(String sequence, double expected) {
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double fraction = BaseUtils.mostFrequentBaseFraction(sequence.getBytes());
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Assert.assertTrue(MathUtils.compareDoubles(fraction, expected) == 0);
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}
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@Test
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public void testTransitionTransversion() {
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logger.warn("Executing testTransitionTransversion");
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Assert.assertTrue( BaseUtils.SNPSubstitutionType( (byte)'A', (byte)'T' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
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Assert.assertTrue( BaseUtils.SNPSubstitutionType( (byte)'A', (byte)'C' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
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Assert.assertTrue( BaseUtils.SNPSubstitutionType( (byte)'A', (byte)'G' ) == BaseUtils.BaseSubstitutionType.TRANSITION );
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Assert.assertTrue( BaseUtils.SNPSubstitutionType( (byte)'C', (byte)'A' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
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Assert.assertTrue( BaseUtils.SNPSubstitutionType( (byte)'C', (byte)'T' ) == BaseUtils.BaseSubstitutionType.TRANSITION );
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Assert.assertTrue( BaseUtils.SNPSubstitutionType( (byte)'C', (byte)'G' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
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Assert.assertTrue( BaseUtils.SNPSubstitutionType( (byte)'T', (byte)'A' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
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Assert.assertTrue( BaseUtils.SNPSubstitutionType( (byte)'T', (byte)'C' ) == BaseUtils.BaseSubstitutionType.TRANSITION );
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Assert.assertTrue( BaseUtils.SNPSubstitutionType( (byte)'T', (byte)'G' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
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Assert.assertTrue( BaseUtils.SNPSubstitutionType( (byte)'G', (byte)'A' ) == BaseUtils.BaseSubstitutionType.TRANSITION );
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Assert.assertTrue( BaseUtils.SNPSubstitutionType( (byte)'G', (byte)'T' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
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Assert.assertTrue( BaseUtils.SNPSubstitutionType( (byte)'G', (byte)'C' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
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Assert.assertTrue( BaseUtils.SNPSubstitutionType( (byte)'a', (byte)'T' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
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Assert.assertTrue( BaseUtils.SNPSubstitutionType( (byte)'a', (byte)'C' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
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Assert.assertTrue( BaseUtils.SNPSubstitutionType( (byte)'A', (byte)'T' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
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Assert.assertTrue( BaseUtils.SNPSubstitutionType( (byte)'A', (byte)'C' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
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Assert.assertTrue( BaseUtils.SNPSubstitutionType( (byte)'A', (byte)'t' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
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Assert.assertTrue( BaseUtils.SNPSubstitutionType( (byte)'A', (byte)'c' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
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Assert.assertTrue( BaseUtils.SNPSubstitutionType( (byte)'a', (byte)'t' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
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Assert.assertTrue( BaseUtils.SNPSubstitutionType( (byte)'a', (byte)'c' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
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}
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@Test
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public void testReverseComplementString() {
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logger.warn("Executing testReverseComplementString");
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compareRCStringToExpected("ACGGT", "ACCGT");
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compareRCStringToExpected("TCGTATATCTCGCTATATATATATAGCTCTAGTATA", "TATACTAGAGCTATATATATATAGCGAGATATACGA");
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compareRCStringToExpected("AAAN", "NTTT");
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}
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private void compareRCStringToExpected(String fw, String rcExp) {
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String rcObs = BaseUtils.simpleReverseComplement(fw);
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Assert.assertTrue(rcObs.equals(rcExp));
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}
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}
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