68 lines
3.8 KiB
Java
Executable File
68 lines
3.8 KiB
Java
Executable File
package org.broadinstitute.sting.utils;
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import org.broadinstitute.sting.BaseTest;
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import org.junit.Test;
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import org.junit.BeforeClass;
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import org.junit.Assert;
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public class BaseUtilsTest extends BaseTest {
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@BeforeClass
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public static 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( 'A', 'T' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
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Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'A', 'C' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
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Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'A', 'G' ) == BaseUtils.BaseSubstitutionType.TRANSITION );
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Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'C', 'A' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
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Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'C', 'T' ) == BaseUtils.BaseSubstitutionType.TRANSITION );
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Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'C', 'G' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
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Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'T', 'A' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
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Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'T', 'C' ) == BaseUtils.BaseSubstitutionType.TRANSITION );
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Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'T', 'G' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
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Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'G', 'A' ) == BaseUtils.BaseSubstitutionType.TRANSITION );
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Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'G', 'T' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
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Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'G', 'C' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
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Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'a', 'T' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
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Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'a', 'C' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
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Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'A', 'T' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
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Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'A', 'C' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
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Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'A', 't' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
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Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'A', 'c' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
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Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'a', 't' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
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Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'a', '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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