110 lines
6.0 KiB
Java
110 lines
6.0 KiB
Java
/*
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* Copyright (c) 2012 The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
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* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.variant.utils;
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import org.broadinstitute.sting.utils.MathUtils;
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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 testConvertIUPACtoN() {
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checkBytesAreEqual(BaseUtils.convertIUPACtoN(new byte[]{'A', 'A', 'A'}, false), new byte[]{'A', 'A', 'A'});
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checkBytesAreEqual(BaseUtils.convertIUPACtoN(new byte[]{'W', 'A', 'A'}, false), new byte[]{'N', 'A', 'A'});
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checkBytesAreEqual(BaseUtils.convertIUPACtoN(new byte[]{'A', 'M', 'A'}, false), new byte[]{'A', 'N', 'A'});
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checkBytesAreEqual(BaseUtils.convertIUPACtoN(new byte[]{'A', 'A', 'K'}, false), new byte[]{'A', 'A', 'N'});
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checkBytesAreEqual(BaseUtils.convertIUPACtoN(new byte[]{'M', 'M', 'M'}, false), new byte[]{'N', 'N', 'N'});
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}
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private void checkBytesAreEqual(final byte[] b1, final byte[] b2) {
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for ( int i = 0; i < b1.length; i++ )
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Assert.assertEquals(b1[i], b2[i]);
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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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