Examples with VDJCGene io.repseq.core.VDJCGene used on opensource projects

Example 16 with VDJCGene

use of io.repseq.core.VDJCGene 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;
}

Example 17 with VDJCGene

use of io.repseq.core.VDJCGene in project mixcr by milaboratory.

the class RunMiXCR method align.

public static AlignResult align(RunMiXCRAnalysis parameters) throws Exception {
    VDJCAlignerParameters alignerParameters = parameters.alignerParameters;
    VDJCAligner aligner = VDJCAligner.createAligner(alignerParameters, parameters.isInputPaired(), alignerParameters.getMergerParameters() != null);
    List<VDJCGene> genes = new ArrayList<>();
    for (VDJCGene gene : VDJCLibraryRegistry.getDefault().getLibrary(parameters.library, parameters.species).getGenes(parameters.chains)) if (alignerParameters.containsRequiredFeature(gene) && (gene.isFunctional() || !parameters.isFunctionalOnly)) {
        genes.add(gene);
        aligner.addGene(gene);
    }
    AlignerReport report = new AlignerReport();
    aligner.setEventsListener(report);
    try (SequenceReaderCloseable<? extends SequenceRead> reader = parameters.getReader()) {
        // start progress reporting
        if (reader instanceof CanReportProgress)
            SmartProgressReporter.startProgressReport("align", (CanReportProgress) reader);
        OutputPort<Chunk<SequenceRead>> mainInputReads = CUtils.buffered((OutputPort) chunked(reader, 64), 16);
        OutputPort<VDJCAlignmentResult> alignments = unchunked(new ParallelProcessor(mainInputReads, chunked(aligner), parameters.threads));
        List<VDJCAlignments> als = new ArrayList<>();
        int ind = 0;
        for (VDJCAlignmentResult t : CUtils.it(new OrderedOutputPort<>(alignments, new Indexer<VDJCAlignmentResult>() {

            @Override
            public long getIndex(VDJCAlignmentResult r) {
                return r.read.getId();
            }
        }))) {
            if (t.alignment != null) {
                t.alignment.setAlignmentsIndex(ind++);
                als.add(t.alignment);
            }
        }
        return new AlignResult(parameters, reader.getNumberOfReads(), report, als, genes, aligner);
    }
}

Example 18 with VDJCGene

use of io.repseq.core.VDJCGene in project mixcr by milaboratory.

the class PartialAlignmentsAssemblerAlignerTest method basicTest1.

@Test
public void basicTest1() throws Exception {
    Well44497b rg = new Well44497b(12312);
    VDJCAlignerParameters rnaSeqParams = VDJCParametersPresets.getByName("rna-seq");
    PartialAlignmentsAssemblerAligner aligner = new PartialAlignmentsAssemblerAligner(rnaSeqParams);
    VDJCLibrary lib = VDJCLibraryRegistry.getDefault().getLibrary("default", "hs");
    for (VDJCGene gene : VDJCLibraryRegistry.getDefault().getLibrary("default", "hs").getGenes()) if (gene.isFunctional())
        aligner.addGene(gene);
    TargetBuilder.VDJCGenes genes = new TargetBuilder.VDJCGenes(lib, "TRBV12-3*00", "TRBD1*00", "TRBJ1-3*00", "TRBC2*00");
    // | 305
    // 250V + 55CDR3 (20V 7N 10D 3N 15J) + 28J + 100C
    NucleotideSequence baseSeq = TargetBuilder.generateSequence(genes, "{CDR3Begin(-250)}V*270 NNNNNNN {DBegin(0)}D*10 NNN {CDR3End(-15):FR4End} {CBegin}C*100", rg);
    int len = 70;
    NucleotideSequence seq1 = baseSeq.getRange(0, len);
    NucleotideSequence seq2 = baseSeq.getRange(245, 245 + len);
    NucleotideSequence seq3 = baseSeq.getRange(320, 320 + len);
    VDJCAlignmentResult<VDJCMultiRead> alignment = aligner.process(MiXCRTestUtils.createMultiRead(seq1, seq2, seq3));
    VDJCAlignments al = alignment.alignment;
    Assert.assertNotNull(al);
    assertInHits(genes.v, al);
    assertInHits(genes.d, al);
    assertInHits(genes.j, al);
    assertInHits(genes.c, al);
    VDJCHit bestV = al.getBestHit(GeneType.Variable);
    VDJCHit bestD = al.getBestHit(GeneType.Diversity);
    VDJCHit bestJ = al.getBestHit(GeneType.Joining);
    VDJCHit bestC = al.getBestHit(GeneType.Constant);
    Assert.assertNotNull(bestV.getAlignment(0));
    Assert.assertNotNull(bestV.getAlignment(1));
    Assert.assertNull(bestV.getAlignment(2));
    Assert.assertNull(bestD.getAlignment(0));
    Assert.assertNotNull(bestD.getAlignment(1));
    Assert.assertNull(bestD.getAlignment(2));
    Assert.assertNull(bestJ.getAlignment(0));
    Assert.assertNotNull(bestJ.getAlignment(1));
    Assert.assertNotNull(bestJ.getAlignment(2));
    Assert.assertNull(bestC.getAlignment(0));
    Assert.assertNull(bestC.getAlignment(1));
    Assert.assertNotNull(bestC.getAlignment(2));
}

Example 19 with VDJCGene

use of io.repseq.core.VDJCGene in project mixcr by milaboratory.

the class VDJCAlignerAbstract method init.

@Override
protected void init() {
    DAlignerParameters dAlignerParameters = parameters.getDAlignerParameters();
    List<VDJCGene> dGenes = genesToAlign.get(GeneType.Diversity);
    if (dAlignerParameters != null && dGenes.size() != 0)
        singleDAligner = new SingleDAligner(dAlignerParameters, genesToAlign.get(GeneType.Diversity));
    vAligner = createKAligner(GeneType.Variable);
    jAligner = createKAligner(GeneType.Joining);
    cAligner = createKAligner(GeneType.Constant);
    Chains chains = new Chains();
    for (VDJCGene gene : getUsedGenes()) chains = chains.merge(gene.getChains());
    filters = new EnumMap<>(GeneType.class);
    for (GeneType geneType : GeneType.VJC_REFERENCE) {
        HashMap<String, BitArray> f = new HashMap<>();
        for (final String chain : chains) {
            BatchAlignerWithBaseWithFilter<NucleotideSequence, VDJCGene, AlignmentHit<NucleotideSequence, VDJCGene>> aligner = getAligner(geneType);
            if (aligner != null)
                f.put(chain, aligner.createFilter(new Filter<VDJCGene>() {

                    @Override
                    public boolean accept(VDJCGene object) {
                        return object.getChains().contains(chain);
                    }
                }));
        }
        filters.put(geneType, f);
    }
}

Example 20 with VDJCGene

use of io.repseq.core.VDJCGene in project repseqio by repseqio.

the class CompileAction method compile.

public static void compile(Path source, Path destination, int surroundings) throws IOException {
    VDJCLibraryRegistry.resetDefaultRegistry();
    VDJCLibraryRegistry reg = VDJCLibraryRegistry.getDefault();
    reg.registerLibraries(source, "lib");
    List<VDJCLibraryData> result = new ArrayList<>();
    for (VDJCLibrary lib : reg.getLoadedLibraries()) {
        VDJCDataUtils.FragmentsBuilder fragmentsBuilder = new VDJCDataUtils.FragmentsBuilder();
        for (KnownSequenceFragmentData fragment : lib.getData().getSequenceFragments()) fragmentsBuilder.addRegion(fragment);
        for (VDJCGene gene : lib.getGenes()) {
            if (!gene.getData().getBaseSequence().isPureOriginalSequence())
                throw new IllegalArgumentException("Don't support mutated sequences yet.");
            URI uri = gene.getData().getBaseSequence().getOrigin();
            Range region = gene.getPartitioning().getContainingRegion();
            region = region.expand(surroundings);
            NucleotideSequence seq;
            try {
                seq = gene.getSequenceProvider().getRegion(region);
            } catch (SequenceProviderIndexOutOfBoundsException e) {
                region = e.getAvailableRange();
                if (region == null)
                    throw new IllegalArgumentException("Wrong anchor points for " + gene.getName() + " ?");
                seq = gene.getSequenceProvider().getRegion(region);
            }
            fragmentsBuilder.addRegion(uri, region, seq);
        }
        result.add(new VDJCLibraryData(lib.getTaxonId(), lib.getData().getSpeciesNames(), lib.getData().getGenes(), lib.getData().getMeta(), fragmentsBuilder.getFragments()));
    }
    VDJCDataUtils.writeToFile(result, destination, true);
    log.info("{} compiled successfully.", source);
}