From b70fd4a2426a21f375776c1de54540a562539423 Mon Sep 17 00:00:00 2001 From: Joel Thibault Date: Wed, 14 Nov 2012 11:08:48 -0500 Subject: [PATCH] Initial testing of the Active Region Traversal contract - TODO: many more tests and test cases --- .../traversals/TraverseActiveRegions.java | 5 +- .../utils/activeregion/ActivityProfile.java | 5 + .../traversals/TraverseActiveRegionsTest.java | 126 ++++++++++++++++++ 3 files changed, 135 insertions(+), 1 deletion(-) create mode 100644 public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java index a2c37944a..4fe83f331 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java +++ b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java @@ -34,6 +34,9 @@ public class TraverseActiveRegions extends TraversalEngine workQueue = new LinkedList(); private final LinkedHashSet myReads = new LinkedHashSet(); + // package access for unit testing + ActivityProfile profile; + @Override public String getTraversalUnits() { return "active regions"; @@ -53,7 +56,7 @@ public class TraverseActiveRegions extends TraversalEngine activeRegions = new LinkedList(); - ActivityProfile profile = new ActivityProfile(engine.getGenomeLocParser(), walker.hasPresetActiveRegions() ); + profile = new ActivityProfile(engine.getGenomeLocParser(), walker.hasPresetActiveRegions() ); ReferenceOrderedView referenceOrderedDataView = getReferenceOrderedView(walker, dataProvider, locusView); diff --git a/public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfile.java b/public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfile.java index e96eb843d..38cfbb38d 100644 --- a/public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfile.java +++ b/public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfile.java @@ -103,6 +103,11 @@ public class ActivityProfile { isActiveList.add(result); } + // for unit testing + public List getActiveList() { + return isActiveList; + } + public int size() { return isActiveList.size(); } diff --git a/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java b/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java new file mode 100644 index 000000000..8740a8b68 --- /dev/null +++ b/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java @@ -0,0 +1,126 @@ +package org.broadinstitute.sting.gatk.traversals; + +import org.testng.Assert; +import net.sf.picard.reference.IndexedFastaSequenceFile; +import net.sf.samtools.SAMRecord; +import net.sf.samtools.SAMSequenceDictionary; +import org.broadinstitute.sting.BaseTest; +import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; +import org.broadinstitute.sting.gatk.contexts.AlignmentContext; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.datasources.providers.LocusShardDataProvider; +import org.broadinstitute.sting.gatk.datasources.reads.MockLocusShard; +import org.broadinstitute.sting.gatk.datasources.reads.Shard; +import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; +import org.broadinstitute.sting.gatk.executive.WindowMaker; +import org.broadinstitute.sting.gatk.iterators.StingSAMIterator; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.ActiveRegionWalker; +import org.broadinstitute.sting.utils.GenomeLoc; +import org.broadinstitute.sting.utils.GenomeLocParser; +import org.broadinstitute.sting.utils.activeregion.ActiveRegion; +import org.broadinstitute.sting.utils.activeregion.ActivityProfileResult; +import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; +import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; +import org.testng.annotations.BeforeClass; +import org.testng.annotations.Test; + + +import java.io.File; +import java.io.FileNotFoundException; +import java.util.ArrayList; +import java.util.List; + +/** + * Created with IntelliJ IDEA. + * User: thibault + * Date: 11/13/12 + * Time: 2:47 PM + */ +public class TraverseActiveRegionsTest extends BaseTest { + + private class DummyActiveRegionWalker extends ActiveRegionWalker { + private final double prob; + + public DummyActiveRegionWalker() { + this.prob = 1.0; + } + + @Override + public ActivityProfileResult isActive(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { + return new ActivityProfileResult(ref.getLocus(), prob); + } + + @Override + public Integer map(ActiveRegion activeRegion, RefMetaDataTracker metaDataTracker) { + return 0; + } + + @Override + public Integer reduceInit() { + return 0; + } + + @Override + public Integer reduce(Integer value, Integer sum) { + return 0; + } + } + + private final TraverseActiveRegions t = new TraverseActiveRegions(); + + private IndexedFastaSequenceFile reference; + private GenomeLocParser genomeLocParser; + private ActiveRegionWalker walker; + + @BeforeClass + private void init() throws FileNotFoundException { + reference = new CachingIndexedFastaSequenceFile(new File(hg19Reference)); + SAMSequenceDictionary dictionary = reference.getSequenceDictionary(); + genomeLocParser = new GenomeLocParser(dictionary); + } + + @Test + public void testAllIntervalsSeen() throws Exception { + List intervals = new ArrayList(); + GenomeLoc interval = genomeLocParser.createGenomeLoc("1", 1, 1); + intervals.add(interval); + + LocusShardDataProvider dataProvider = createDataProvider(intervals); + + t.traverse(walker, dataProvider, 0); + + boolean allGenomeLocsSeen = true; + for (GenomeLoc loc : intervals) { + boolean thisGenomeLocSeen = false; + for (ActivityProfileResult active : t.profile.getActiveList()) { + if (loc.equals(active.getLoc())) { + thisGenomeLocSeen = true; + break; + } + } + if (!thisGenomeLocSeen) { + allGenomeLocsSeen = false; + break; + } + } + + Assert.assertTrue(allGenomeLocsSeen, "Some intervals missing from activity profile"); + } + + private LocusShardDataProvider createDataProvider(List intervals) { + walker = new DummyActiveRegionWalker(); + + StingSAMIterator iterator = ArtificialSAMUtils.createReadIterator(new ArrayList()); + Shard shard = new MockLocusShard(genomeLocParser, intervals); + WindowMaker windowMaker = new WindowMaker(shard, genomeLocParser,iterator,shard.getGenomeLocs()); + WindowMaker.WindowMakerIterator window = windowMaker.next(); + + GenomeAnalysisEngine engine = new GenomeAnalysisEngine(); + //engine.setReferenceDataSource(reference); + engine.setGenomeLocParser(genomeLocParser); + t.initialize(engine); + + return new LocusShardDataProvider(shard, null, genomeLocParser, window.getLocus(), window, reference, new ArrayList()); + } +}