Unit tests for the reference views. Partially addresses GSA-25.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@833 348d0f76-0448-11de-a6fe-93d51630548a
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package org.broadinstitute.sting.gatk.dataSources.providers;
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import org.junit.Test;
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import org.junit.Assert;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.gatk.dataSources.shards.Shard;
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import org.broadinstitute.sting.gatk.dataSources.shards.LocusShard;
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import org.broadinstitute.sting.gatk.iterators.GenomeLocusIterator;
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import edu.mit.broad.picard.reference.ReferenceSequence;
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import net.sf.samtools.util.StringUtil;
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/**
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* User: hanna
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* Date: May 27, 2009
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* Time: 11:10:00 AM
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* BROAD INSTITUTE SOFTWARE COPYRIGHT NOTICE AND AGREEMENT
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* Software and documentation are copyright 2005 by the Broad Institute.
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* All rights are reserved.
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*
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* Users acknowledge that this software is supplied without any warranty or support.
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* The Broad Institute is not responsible for its use, misuse, or
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* functionality.
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*/
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/**
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* Tests for viewing the reference from the perspective of a locus.
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*/
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public class LocusReferenceViewTest extends ReferenceViewTemplate {
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/**
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* Multiple-base pair queries should generate exceptions.
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*/
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@Test(expected=InvalidPositionException.class)
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public void testSingleBPFailure() {
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Shard shard = new LocusShard( new GenomeLoc(0,1,50) );
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ShardDataProvider dataProvider = new ShardDataProvider(shard,null,sequenceFile,null);
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LocusReferenceView view = new LocusReferenceView(dataProvider);
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view.getReferenceBase(shard.getGenomeLoc());
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}
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/**
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* Queries outside the bounds of the shard should generate an error.
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*/
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@Test(expected=InvalidPositionException.class)
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public void testBoundsFailure() {
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Shard shard = new LocusShard( new GenomeLoc(0,1,50) );
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ShardDataProvider dataProvider = new ShardDataProvider(shard,null,sequenceFile,null);
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LocusReferenceView view = new LocusReferenceView(dataProvider);
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view.getReferenceBase(new GenomeLoc(0,51));
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}
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/**
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* Compares the contents of the fasta and view at a specified location.
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* @param loc
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*/
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protected void validateLocation( GenomeLoc loc ) {
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Shard shard = new LocusShard( loc );
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GenomeLocusIterator shardIterator = new GenomeLocusIterator(shard.getGenomeLoc());
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ShardDataProvider dataProvider = new ShardDataProvider(shard,null,sequenceFile,null);
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LocusReferenceView view = new LocusReferenceView(dataProvider);
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while( shardIterator.hasNext() ) {
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GenomeLoc locus = shardIterator.next();
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ReferenceSequence expectedAsSeq = sequenceFile.getSubsequenceAt(locus.getContig(),locus.getStart(),locus.getStop());
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char expected = StringUtil.bytesToString(expectedAsSeq.getBases()).charAt(0);
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char actual = view.getReferenceBase(locus);
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Assert.assertEquals(String.format("Value of base at position %s in shard %s does not match expected",locus.toString(),shard.getGenomeLoc()),
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expected,
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actual);
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}
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}
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}
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package org.broadinstitute.sting.gatk.dataSources.providers;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.junit.Assert;
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import net.sf.samtools.SAMRecord;
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import net.sf.samtools.SAMFileHeader;
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import net.sf.samtools.Cigar;
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import net.sf.samtools.CigarElement;
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import net.sf.samtools.CigarOperator;
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import net.sf.samtools.util.StringUtil;
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import edu.mit.broad.picard.reference.ReferenceSequence;
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/**
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* User: hanna
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* Date: May 27, 2009
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* Time: 1:04:27 PM
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* BROAD INSTITUTE SOFTWARE COPYRIGHT NOTICE AND AGREEMENT
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* Software and documentation are copyright 2005 by the Broad Institute.
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* All rights are reserved.
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*
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* Users acknowledge that this software is supplied without any warranty or support.
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* The Broad Institute is not responsible for its use, misuse, or
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* functionality.
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*/
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/**
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* Test reading the reference for a given read.
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*/
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public class ReadReferenceViewTest extends ReferenceViewTemplate {
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/**
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* Compares the contents of the fasta and view at a specified location.
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* @param loc
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*/
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protected void validateLocation( GenomeLoc loc ) {
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SAMRecord read = buildSAMRecord( loc.getContig(), (int)loc.getStart(), (int)loc.getStop() );
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ShardDataProvider dataProvider = new ShardDataProvider(null,null,sequenceFile,null);
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ReadReferenceView view = new ReadReferenceView(dataProvider);
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ReferenceSequence expectedAsSeq = sequenceFile.getSubsequenceAt(loc.getContig(),loc.getStart(),loc.getStop());
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char[] expected = StringUtil.bytesToString(expectedAsSeq.getBases()).toCharArray();
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char[] actual = view.getReferenceBases(read);
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Assert.assertArrayEquals(String.format("Base array at in shard %s does not match expected",loc.toString()),
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expected,
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actual);
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}
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/**
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* Build a SAM record featuring the absolute minimum required dataset.
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* TODO: Blatantly copied from LocusViewTemplate. Refactor these into a set of tools.
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* @param contig Contig to populate.
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* @param alignmentStart start of alignment
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* @param alignmentEnd end of alignment
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* @return New SAM Record
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*/
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protected SAMRecord buildSAMRecord( String contig, int alignmentStart, int alignmentEnd ) {
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SAMFileHeader header = new SAMFileHeader();
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header.setSequenceDictionary(sequenceFile.getSequenceDictionary());
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SAMRecord record = new SAMRecord(header);
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record.setReferenceIndex(sequenceFile.getSequenceDictionary().getSequenceIndex(contig));
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record.setAlignmentStart(alignmentStart);
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Cigar cigar = new Cigar();
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cigar.add(new CigarElement(alignmentEnd-alignmentStart+1, CigarOperator.M));
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record.setCigar(cigar);
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return record;
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}
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}
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package org.broadinstitute.sting.gatk.dataSources.providers;
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import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.BaseTest;
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import org.junit.BeforeClass;
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import org.junit.Test;
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import java.io.FileNotFoundException;
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import java.io.File;
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import net.sf.samtools.SAMSequenceRecord;
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/**
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* User: hanna
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* Date: May 27, 2009
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* Time: 1:12:35 PM
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* BROAD INSTITUTE SOFTWARE COPYRIGHT NOTICE AND AGREEMENT
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* Software and documentation are copyright 2005 by the Broad Institute.
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* All rights are reserved.
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*
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* Users acknowledge that this software is supplied without any warranty or support.
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* The Broad Institute is not responsible for its use, misuse, or
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* functionality.
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*/
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/**
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* Template for testing reference views (ReadReferenceView and LocusReferenceView).
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*/
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public abstract class ReferenceViewTemplate extends BaseTest {
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/**
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* The fasta, for comparison.
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*/
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protected static IndexedFastaSequenceFile sequenceFile = null;
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//
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// The bulk of sequence retrieval is tested by IndexedFastaSequenceFile, but we'll run a few spot
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// checks here to make sure that data is flowing through the LocusReferenceView.
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/**
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* Initialize the fasta.
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*/
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@BeforeClass
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public static void initialize() throws FileNotFoundException {
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sequenceFile = new IndexedFastaSequenceFile( new File(seqLocation + "/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta") );
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GenomeLoc.setupRefContigOrdering(sequenceFile);
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}
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/**
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* Test the initial fasta location.
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*/
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@Test
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public void testReferenceStart() {
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validateLocation( new GenomeLoc(0,1,25) );
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}
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/**
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* Test the end of a contig.
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*/
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@Test
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public void testReferenceEnd() {
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// Test the last 25 bases of the first contig.
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SAMSequenceRecord selectedContig = sequenceFile.getSequenceDictionary().getSequences().get(sequenceFile.getSequenceDictionary().getSequences().size()-1);
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final long contigStart = selectedContig.getSequenceLength() - 24;
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final long contigStop = selectedContig.getSequenceLength();
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validateLocation( new GenomeLoc(selectedContig.getSequenceIndex(),contigStart,contigStop) );
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}
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/**
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* Test the start of the middle contig.
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*/
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@Test
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public void testContigStart() {
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// Test the last 25 bases of the first contig.
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int contigPosition = sequenceFile.getSequenceDictionary().getSequences().size()/2;
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SAMSequenceRecord selectedContig = sequenceFile.getSequenceDictionary().getSequences().get(contigPosition);
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validateLocation( new GenomeLoc(selectedContig.getSequenceIndex(),1,25) );
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}
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/**
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* Test the end of the middle contig.
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*/
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@Test
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public void testContigEnd() {
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// Test the last 25 bases of the first contig.
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int contigPosition = sequenceFile.getSequenceDictionary().getSequences().size()/2;
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SAMSequenceRecord selectedContig = sequenceFile.getSequenceDictionary().getSequences().get(contigPosition);
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final long contigStart = selectedContig.getSequenceLength() - 24;
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final long contigStop = selectedContig.getSequenceLength();
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validateLocation( new GenomeLoc(selectedContig.getSequenceIndex(),contigStart,contigStop) );
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}
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protected abstract void validateLocation( GenomeLoc loc );
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}
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