Search in sources :

Example 41 with NucleotideSequence

use of com.milaboratory.core.sequence.NucleotideSequence in project mixcr by milaboratory.

the class CloneAssemblerRunnerTest method runFullPipeline.

private static CloneSet runFullPipeline(String... fastqFiles) throws IOException, InterruptedException {
    // building alignments
    VDJCAlignerParameters alignerParameters = VDJCParametersPresets.getByName("default");
    VDJCAligner aligner = fastqFiles.length == 1 ? new VDJCAlignerS(alignerParameters) : new VDJCAlignerWithMerge(alignerParameters);
    for (VDJCGene gene : VDJCLibraryRegistry.getDefault().getLibrary("mi", "hs").getGenes(Chains.IGH)) if (alignerParameters.containsRequiredFeature(gene))
        aligner.addGene(gene);
    SequenceReader reader;
    if (fastqFiles.length == 1)
        reader = new SingleFastqReader(CloneAssemblerRunnerTest.class.getClassLoader().getResourceAsStream(fastqFiles[0]), true);
    else
        reader = new PairedFastqReader(CloneAssemblerRunnerTest.class.getClassLoader().getResourceAsStream(fastqFiles[0]), CloneAssemblerRunnerTest.class.getClassLoader().getResourceAsStream(fastqFiles[1]), true);
    // write alignments to byte array
    ByteArrayOutputStream alignmentsSerialized = new ByteArrayOutputStream();
    try (VDJCAlignmentsWriter writer = new VDJCAlignmentsWriter(alignmentsSerialized)) {
        writer.header(aligner);
        for (Object read : CUtils.it(reader)) {
            VDJCAlignmentResult result = (VDJCAlignmentResult) aligner.process((SequenceRead) read);
            if (result.alignment != null)
                writer.write(result.alignment);
        }
    }
    AlignmentsProvider alignmentsProvider = AlignmentsProvider.Util.createProvider(alignmentsSerialized.toByteArray(), VDJCLibraryRegistry.getDefault());
    LinearGapAlignmentScoring<NucleotideSequence> scoring = new LinearGapAlignmentScoring<>(NucleotideSequence.ALPHABET, 5, -9, -12);
    CloneFactoryParameters factoryParameters = new CloneFactoryParameters(new VJCClonalAlignerParameters(0.8f, scoring, 5), new VJCClonalAlignerParameters(0.8f, scoring, 5), null, new DAlignerParameters(GeneFeature.DRegion, 0.85f, 30.0f, 3, scoring));
    CloneAssemblerParameters assemblerParameters = new CloneAssemblerParameters(new GeneFeature[] { GeneFeature.CDR3 }, 12, QualityAggregationType.Average, new CloneClusteringParameters(2, 1, TreeSearchParameters.ONE_MISMATCH, new RelativeConcentrationFilter(1.0E-6)), factoryParameters, true, true, false, 0.4, true, (byte) 20, .8, "2 of 6", (byte) 15);
    System.out.println(GlobalObjectMappers.toOneLine(assemblerParameters));
    CloneAssemblerRunner assemblerRunner = new CloneAssemblerRunner(alignmentsProvider, new CloneAssembler(assemblerParameters, true, aligner.getUsedGenes(), alignerParameters), 2);
    SmartProgressReporter.startProgressReport(assemblerRunner);
    assemblerRunner.run();
    CloneSet cloneSet = assemblerRunner.getCloneSet(null);
    ByteArrayOutputStream bos = new ByteArrayOutputStream();
    CloneSetIO.write(cloneSet, bos);
    CloneSet cloneSetDeserialized = CloneSetIO.readClns(new ByteArrayInputStream(bos.toByteArray()));
    assertCSEquals(cloneSet, cloneSetDeserialized);
    OutputPortCloseable<ReadToCloneMapping> rrr = assemblerRunner.assembler.getAssembledReadsPort();
    ReadToCloneMapping take;
    while ((take = rrr.take()) != null) System.out.println(take);
    return cloneSet;
}
Also used : SingleFastqReader(com.milaboratory.core.io.sequence.fastq.SingleFastqReader) VDJCAlignmentsWriter(com.milaboratory.mixcr.basictypes.VDJCAlignmentsWriter) CloneSet(com.milaboratory.mixcr.basictypes.CloneSet) LinearGapAlignmentScoring(com.milaboratory.core.alignment.LinearGapAlignmentScoring) ByteArrayOutputStream(java.io.ByteArrayOutputStream) ByteArrayInputStream(java.io.ByteArrayInputStream) NucleotideSequence(com.milaboratory.core.sequence.NucleotideSequence) SequenceRead(com.milaboratory.core.io.sequence.SequenceRead) SequenceReader(com.milaboratory.core.io.sequence.SequenceReader) PairedFastqReader(com.milaboratory.core.io.sequence.fastq.PairedFastqReader)

Example 42 with NucleotideSequence

use of com.milaboratory.core.sequence.NucleotideSequence in project mixcr by milaboratory.

the class ClonalSequenceTest method testIsCompatible2.

@Test
public void testIsCompatible2() throws Exception {
    RandomGenerator generator = new Well1024a();
    Mutations<NucleotideSequence> muts = Mutations.decode("", NucleotideSequence.ALPHABET);
    for (int i = 0; i < 100; i++) {
        ClonalSequence c1 = createRandom(5 + generator.nextInt(10), generator);
        Assert.assertTrue(c1.isCompatible(c1, muts));
    }
}
Also used : NucleotideSequence(com.milaboratory.core.sequence.NucleotideSequence) RandomGenerator(org.apache.commons.math3.random.RandomGenerator) Well1024a(org.apache.commons.math3.random.Well1024a) Test(org.junit.Test)

Example 43 with NucleotideSequence

use of com.milaboratory.core.sequence.NucleotideSequence in project mixcr by milaboratory.

the class ClonalSequenceTest method createRandomTestDara.

private TestData createRandomTestDara(int size, RandomGenerator random) {
    MutationsBuilder<NucleotideSequence> builder = new MutationsBuilder<>(NucleotideSequence.ALPHABET);
    NSequenceWithQuality[] c1 = new NSequenceWithQuality[size];
    NSequenceWithQuality[] c2 = new NSequenceWithQuality[size];
    int offset = 0;
    for (int i = 0; i < size; ++i) {
        NucleotideSequence s1 = TestUtil.randomSequence(NucleotideSequence.ALPHABET, random, 5, 15);
        Mutations<NucleotideSequence> muts = MutationsGenerator.generateMutations(s1, MutationModels.getEmpiricalNucleotideMutationModel(), 1, s1.size() - 1);
        NucleotideSequence s2 = muts.mutate(s1);
        c1[i] = new NSequenceWithQuality(s1, SequenceQuality.getUniformQuality((byte) 0, s1.size()));
        c2[i] = new NSequenceWithQuality(s2, SequenceQuality.getUniformQuality((byte) 0, s2.size()));
        builder.append(muts.move(offset));
        offset += s1.size();
    }
    return new TestData(new ClonalSequence(c1), new ClonalSequence(c2), builder.createAndDestroy());
}
Also used : NucleotideSequence(com.milaboratory.core.sequence.NucleotideSequence) NSequenceWithQuality(com.milaboratory.core.sequence.NSequenceWithQuality) MutationsBuilder(com.milaboratory.core.mutations.MutationsBuilder)

Example 44 with NucleotideSequence

use of com.milaboratory.core.sequence.NucleotideSequence in project mixcr by milaboratory.

the class ClonalSequenceTest method create.

private ClonalSequence create(String... strings) {
    NSequenceWithQuality[] data = new NSequenceWithQuality[strings.length];
    for (int i = 0; i < strings.length; ++i) {
        NucleotideSequence s = new NucleotideSequence(strings[i]);
        SequenceQuality q = SequenceQuality.getUniformQuality((byte) 0, s.size());
        data[i] = new NSequenceWithQuality(s, q);
    }
    return new ClonalSequence(data);
}
Also used : SequenceQuality(com.milaboratory.core.sequence.SequenceQuality) NSequenceWithQuality(com.milaboratory.core.sequence.NSequenceWithQuality) NucleotideSequence(com.milaboratory.core.sequence.NucleotideSequence)

Example 45 with NucleotideSequence

use of com.milaboratory.core.sequence.NucleotideSequence in project mixcr by milaboratory.

the class TargetMerger method merge.

@SuppressWarnings("unchecked")
public AlignedTarget merge(AlignedTarget targetLeft, AlignedTarget targetRight, int offset, OverlapType overlapType, int nMismatches) {
    if (offset < 0)
        return merge(targetRight, targetLeft, -offset, overlapType, nMismatches);
    final NSequenceWithQuality mergedTarget = merger.overlap(targetLeft.getTarget(), targetRight.getTarget(), offset);
    EnumMap<GeneType, VDJCHit[]> result = new EnumMap<>(GeneType.class);
    for (GeneType geneType : GeneType.VJC_REFERENCE) {
        final BatchAlignerWithBaseParameters bp = ((KGeneAlignmentParameters) alignerParameters.getGeneAlignerParameters(geneType)).getParameters();
        final VDJCHit[] leftHits = targetLeft.getAlignments().getHits(geneType);
        final VDJCHit[] rightHits = targetRight.getAlignments().getHits(geneType);
        GeneFeature alignedFeature = leftHits.length == 0 ? rightHits.length == 0 ? null : rightHits[0].getAlignedFeature() : leftHits[0].getAlignedFeature();
        Map<VDJCGeneId, HitMappingRecord> map = extractHitsMapping(targetLeft, targetRight, geneType);
        ArrayList<VDJCHit> resultingHits = new ArrayList<>();
        for (Map.Entry<VDJCGeneId, HitMappingRecord> mE : map.entrySet()) {
            final VDJCGene gene = mE.getValue().gene;
            Alignment<NucleotideSequence> mergedAl = merge(bp.getScoring(), extractBandedWidth(bp), mergedTarget.getSequence(), offset, mE.getValue().alignments[0], mE.getValue().alignments[1]);
            resultingHits.add(new VDJCHit(gene, mergedAl, alignedFeature));
        }
        Collections.sort(resultingHits);
        // final float relativeMinScore = extractRelativeMinScore(bp);
        // int threshold = (int) (resultingHits.size() > 0 ? resultingHits.get(0).getScore() * relativeMinScore : 0);
        // for (int i = resultingHits.size() - 1; i > 0; --i)
        // if (resultingHits.get(i).getScore() < threshold)
        // resultingHits.remove(i);
        result.put(geneType, resultingHits.toArray(new VDJCHit[resultingHits.size()]));
    }
    VDJCAlignments alignments = new VDJCAlignments(result, new NSequenceWithQuality[] { mergedTarget }, new SequenceHistory[] { new SequenceHistory.Merge(overlapType, targetLeft.getHistory(), targetRight.getHistory(), offset, nMismatches) }, VDJCAlignments.mergeOriginalReads(targetLeft.getAlignments(), targetRight.getAlignments()));
    AlignedTarget resultTarget = new AlignedTarget(alignments, 0);
    for (BPoint bPoint : BPoint.values()) {
        int leftPoint = targetLeft.getBPoint(bPoint);
        int rightPoint = targetRight.getBPoint(bPoint);
        if (leftPoint != -1 && rightPoint != -1)
            throw new IllegalArgumentException("Same bPoint defined in both input targets.");
        else if (leftPoint != -1)
            resultTarget = resultTarget.setBPoint(bPoint, leftPoint);
        else if (rightPoint != -1)
            resultTarget = resultTarget.setBPoint(bPoint, offset + rightPoint);
    }
    return resultTarget;
}
Also used : GeneFeature(io.repseq.core.GeneFeature) SequenceHistory(com.milaboratory.mixcr.basictypes.SequenceHistory) VDJCGeneId(io.repseq.core.VDJCGeneId) NSequenceWithQuality(com.milaboratory.core.sequence.NSequenceWithQuality) VDJCAlignments(com.milaboratory.mixcr.basictypes.VDJCAlignments) BatchAlignerWithBaseParameters(com.milaboratory.core.alignment.batch.BatchAlignerWithBaseParameters) KGeneAlignmentParameters(com.milaboratory.mixcr.vdjaligners.KGeneAlignmentParameters) NucleotideSequence(com.milaboratory.core.sequence.NucleotideSequence) VDJCGene(io.repseq.core.VDJCGene) GeneType(io.repseq.core.GeneType) VDJCHit(com.milaboratory.mixcr.basictypes.VDJCHit)

Aggregations

NucleotideSequence (com.milaboratory.core.sequence.NucleotideSequence)81 Test (org.junit.Test)32 Range (com.milaboratory.core.Range)19 VDJCGene (io.repseq.core.VDJCGene)15 GeneType (io.repseq.core.GeneType)14 NSequenceWithQuality (com.milaboratory.core.sequence.NSequenceWithQuality)13 GeneFeature (io.repseq.core.GeneFeature)9 VDJCAlignments (com.milaboratory.mixcr.basictypes.VDJCAlignments)8 VDJCHit (com.milaboratory.mixcr.basictypes.VDJCHit)8 ReferencePoint (io.repseq.core.ReferencePoint)7 VDJCLibrary (io.repseq.core.VDJCLibrary)7 ArrayList (java.util.ArrayList)7 VDJCAlignerParameters (com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters)6 AlignmentHit (com.milaboratory.core.alignment.batch.AlignmentHit)5 PairedRead (com.milaboratory.core.io.sequence.PairedRead)5 AminoAcidSequence (com.milaboratory.core.sequence.AminoAcidSequence)5 Path (java.nio.file.Path)5 Alignment (com.milaboratory.core.alignment.Alignment)4 Pattern (java.util.regex.Pattern)4 AlignmentHelper (com.milaboratory.core.alignment.AlignmentHelper)3