273 lines
12 KiB
Java
Executable File
273 lines
12 KiB
Java
Executable File
package org.broadinstitute.sting.utils.fasta;
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import org.junit.BeforeClass;
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import org.junit.Before;
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import org.junit.Test;
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import org.junit.Assert;
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import org.broadinstitute.sting.BaseTest;
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import java.io.File;
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import java.io.FileNotFoundException;
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import edu.mit.broad.picard.reference.ReferenceSequence;
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import edu.mit.broad.picard.PicardException;
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import net.sf.samtools.util.StringUtil;
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/**
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* Created by IntelliJ IDEA.
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* User: hanna
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* Date: Apr 14, 2009
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* Time: 2:37:29 PM
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* To change this template use File | Settings | File Templates.
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*/
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public class IndexedFastaSequenceFileTest extends BaseTest {
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private static String sequenceFileName;
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private IndexedFastaSequenceFile sequenceFile = null;
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private final String firstBasesOfChrM = "GATCACAGGTCTATCACCCT";
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private final String extendedBasesOfChrM = "GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCAT" +
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"TTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTG" +
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"GAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATT";
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private final String firstBasesOfChr1 = "taaccctaaccctaacccta";
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private final String firstBasesOfChr8 = "GCAATTATGACACAAAAAAT";
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@BeforeClass
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public static void initialize() {
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sequenceFileName = seqLocation + "/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta";
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}
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@Before
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public void doForEachTest() throws FileNotFoundException {
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sequenceFile = new IndexedFastaSequenceFile( new File(sequenceFileName) );
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}
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@Test
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public void testOpenFile() {
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long startTime = System.currentTimeMillis();
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Assert.assertNotNull( sequenceFile );
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long endTime = System.currentTimeMillis();
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System.err.printf("testOpenFile runtime: %dms%n", (endTime - startTime)) ;
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}
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@Test
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public void testFirstSequence() {
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long startTime = System.currentTimeMillis();
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ReferenceSequence sequence = sequenceFile.getSubsequenceAt("chrM",1,firstBasesOfChrM.length());
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long endTime = System.currentTimeMillis();
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Assert.assertEquals("Sequence contig is not correct", sequence.getName(), "chrM");
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Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 0);
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Assert.assertEquals( "First n bases of chrM are incorrect",
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firstBasesOfChrM,
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StringUtil.bytesToString( sequence.getBases() ) );
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System.err.printf("testFirstSequence runtime: %dms%n", (endTime - startTime)) ;
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}
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@Test
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public void testFirstSequenceExtended() {
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long startTime = System.currentTimeMillis();
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ReferenceSequence sequence = sequenceFile.getSubsequenceAt("chrM",1,extendedBasesOfChrM.length());
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long endTime = System.currentTimeMillis();
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Assert.assertEquals("Sequence contig is not correct", sequence.getName(), "chrM");
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Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 0);
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Assert.assertEquals( "First n bases of chrM are incorrect",
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extendedBasesOfChrM,
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StringUtil.bytesToString(sequence.getBases()) );
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System.err.printf("testFirstSequenceExtended runtime: %dms%n", (endTime - startTime)) ;
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}
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@Test
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public void testReadStartingInCenterOfFirstLine() {
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final int bytesToChopOff = 5;
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String truncated = extendedBasesOfChrM.substring(bytesToChopOff);
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long startTime = System.currentTimeMillis();
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ReferenceSequence sequence = sequenceFile.getSubsequenceAt("chrM",
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bytesToChopOff + 1,
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bytesToChopOff + truncated.length());
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long endTime = System.currentTimeMillis();
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Assert.assertEquals("Sequence contig is not correct", sequence.getName(), "chrM");
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Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 0);
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Assert.assertEquals( "First n bases of chrM are incorrect",
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truncated,
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StringUtil.bytesToString( sequence.getBases() ) );
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System.err.printf("testReadStartingInCenterOfFirstLine runtime: %dms%n", (endTime - startTime)) ;
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}
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@Test
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public void testReadStartingInCenterOfMiddleLine() {
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final int bytesToChopOff = 120;
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String truncated = extendedBasesOfChrM.substring(bytesToChopOff);
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long startTime = System.currentTimeMillis();
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ReferenceSequence sequence = sequenceFile.getSubsequenceAt("chrM",
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bytesToChopOff + 1,
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bytesToChopOff + truncated.length());
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long endTime = System.currentTimeMillis();
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Assert.assertEquals("Sequence contig is not correct", sequence.getName(), "chrM");
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Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 0);
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Assert.assertEquals( "First n bases of chrM are incorrect",
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truncated,
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StringUtil.bytesToString( sequence.getBases() ) );
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System.err.printf("testReadStartingInCenterOfMiddleLine runtime: %dms%n", (endTime - startTime)) ;
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}
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@Test
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public void testFirstCompleteContigRead() {
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FastaSequenceFile2 originalSequenceFile = new FastaSequenceFile2(new File(sequenceFileName));
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ReferenceSequence expectedSequence = originalSequenceFile.nextSequence();
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long startTime = System.currentTimeMillis();
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ReferenceSequence sequence = sequenceFile.getSequence("chrM");
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long endTime = System.currentTimeMillis();
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Assert.assertEquals("Sequence contig is not correct", sequence.getName(), "chrM");
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Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 0);
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Assert.assertEquals("chrM is incorrect",
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StringUtil.bytesToString(expectedSequence.getBases()),
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StringUtil.bytesToString(sequence.getBases()) );
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System.err.printf("testFirstCompleteContigRead runtime: %dms%n", (endTime - startTime)) ;
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}
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@Test(expected= PicardException.class)
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public void testReadThroughEndOfContig() {
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long startTime = System.currentTimeMillis();
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try {
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ReferenceSequence sequence = sequenceFile.getSubsequenceAt("chrM",16500,16600);
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}
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finally {
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long endTime = System.currentTimeMillis();
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System.err.printf("testReadThroughEndOfContig runtime: %dms%n", (endTime - startTime)) ;
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}
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}
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@Test(expected= PicardException.class)
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public void testReadPastEndOfContig() {
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long startTime = System.currentTimeMillis();
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try {
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ReferenceSequence sequence = sequenceFile.getSubsequenceAt("chrM",16800,16900);
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}
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finally {
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long endTime = System.currentTimeMillis();
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System.err.printf("testReadPastEndOfContig runtime: %dms%n", (endTime - startTime)) ;
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}
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}
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@Test
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public void testMiddleCompleteContigRead() {
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FastaSequenceFile2 originalSequenceFile = new FastaSequenceFile2(new File(sequenceFileName));
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originalSequenceFile.seekToContig("chrY");
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ReferenceSequence expectedSequence = originalSequenceFile.nextSequence();
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long startTime = System.currentTimeMillis();
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ReferenceSequence sequence = sequenceFile.getSequence("chrY");
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long endTime = System.currentTimeMillis();
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Assert.assertEquals("Sequence contig is not correct", sequence.getName(), "chrY");
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Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 24);
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Assert.assertEquals("chrY is incorrect",
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StringUtil.bytesToString(expectedSequence.getBases()),
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StringUtil.bytesToString(sequence.getBases()) );
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System.err.printf("testMiddleCompleteContigRead runtime: %dms%n", (endTime - startTime)) ;
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}
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@Test
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public void testLastCompleteContigRead() {
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FastaSequenceFile2 originalSequenceFile = new FastaSequenceFile2(new File(sequenceFileName));
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originalSequenceFile.seekToContig("chrX_random");
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ReferenceSequence expectedSequence = originalSequenceFile.nextSequence();
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long startTime = System.currentTimeMillis();
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ReferenceSequence sequence = sequenceFile.getSequence("chrX_random");
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long endTime = System.currentTimeMillis();
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Assert.assertEquals("Sequence contig is not correct", sequence.getName(), "chrX_random");
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Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 44);
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Assert.assertEquals("chrX_random is incorrect",
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StringUtil.bytesToString(expectedSequence.getBases()),
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StringUtil.bytesToString(sequence.getBases()) );
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System.err.printf("testLastCompleteContigRead runtime: %dms%n", (endTime - startTime)) ;
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}
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@Test
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public void testFirstOfChr1() {
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long startTime = System.currentTimeMillis();
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ReferenceSequence sequence = sequenceFile.getSubsequenceAt("chr1",1,firstBasesOfChr1.length());
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long endTime = System.currentTimeMillis();
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Assert.assertEquals("Sequence contig is not correct", sequence.getName(), "chr1");
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Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 1);
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Assert.assertEquals( "First n bases of chr1 are incorrect",
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firstBasesOfChr1,
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StringUtil.bytesToString( sequence.getBases() ) );
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System.err.printf("testFirstOfChr1 runtime: %dms%n", (endTime - startTime)) ;
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}
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@Test
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public void testFirstOfChr8() {
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long startTime = System.currentTimeMillis();
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ReferenceSequence sequence = sequenceFile.getSubsequenceAt("chr8",1,firstBasesOfChr8.length());
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long endTime = System.currentTimeMillis();
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Assert.assertEquals("Sequence contig is not correct", sequence.getName(), "chr8");
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Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 8);
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Assert.assertEquals( "First n bases of chr8 are incorrect",
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firstBasesOfChr8,
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StringUtil.bytesToString( sequence.getBases() ) );
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System.err.printf("testFirstOfChr8 runtime: %dms%n", (endTime - startTime)) ;
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}
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@Test
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public void testFirstElementOfIterator() {
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FastaSequenceFile2 originalSequenceFile = new FastaSequenceFile2(new File(sequenceFileName));
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ReferenceSequence expectedSequence = originalSequenceFile.nextSequence();
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long startTime = System.currentTimeMillis();
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ReferenceSequence sequence = sequenceFile.nextSequence();
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long endTime = System.currentTimeMillis();
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Assert.assertEquals("Sequence contig is not correct", sequence.getName(), "chrM");
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Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 0);
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Assert.assertEquals("chrM is incorrect",
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StringUtil.bytesToString(expectedSequence.getBases()),
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StringUtil.bytesToString(sequence.getBases()) );
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System.err.printf("testFirstElementOfIterator runtime: %dms%n", (endTime - startTime)) ;
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}
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@Test
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public void testNextElementOfIterator() {
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FastaSequenceFile2 originalSequenceFile = new FastaSequenceFile2(new File(sequenceFileName));
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// Skip past the first one and load the second one.
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originalSequenceFile.nextSequence();
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ReferenceSequence expectedSequence = originalSequenceFile.nextSequence();
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long startTime = System.currentTimeMillis();
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sequenceFile.nextSequence();
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ReferenceSequence sequence = sequenceFile.nextSequence();
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long endTime = System.currentTimeMillis();
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Assert.assertEquals("Sequence contig is not correct", sequence.getName(), "chr1");
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Assert.assertEquals("Sequence contig index is not correct", sequence.getContigIndex(), 1);
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Assert.assertEquals("chr1 is incorrect",
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StringUtil.bytesToString(expectedSequence.getBases()),
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StringUtil.bytesToString(sequence.getBases()) );
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System.err.printf("testNextElementOfIterator runtime: %dms%n", (endTime - startTime)) ;
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}
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}
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