Examples with VDJCAlignments com.milaboratory.mixcr.basictypes.VDJCAlignments used on opensource projects

Example 21 with VDJCAlignments

use of com.milaboratory.mixcr.basictypes.VDJCAlignments 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 22 with VDJCAlignments

use of com.milaboratory.mixcr.basictypes.VDJCAlignments 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 23 with VDJCAlignments

use of com.milaboratory.mixcr.basictypes.VDJCAlignments in project mixcr by milaboratory.

the class ActionFilterAlignments method go.

@Override
public void go(ActionHelper helper) throws Exception {
    try (VDJCAlignmentsReader reader = parameters.getInput();
        VDJCAlignmentsWriter writer = parameters.getOutput()) {
        CanReportProgress progress = reader;
        OutputPort<VDJCAlignments> sReads = reader;
        if (parameters.limit != 0) {
            sReads = new CountLimitingOutputPort<>(sReads, parameters.limit);
            progress = SmartProgressReporter.extractProgress((CountLimitingOutputPort<?>) sReads);
        }
        writer.header(reader.getParameters(), reader.getUsedGenes());
        SmartProgressReporter.startProgressReport("Filtering", progress);
        int total = 0, passed = 0;
        final AlignmentsFilter filter = parameters.getFilter();
        for (VDJCAlignments al : CUtils.it(CUtils.buffered(sReads, 2048))) {
            ++total;
            if (filter.accept(al)) {
                writer.write(al);
                ++passed;
            }
        }
        writer.setNumberOfProcessedReads(reader.getNumberOfReads());
        System.out.printf("%s alignments analysed\n", total);
        System.out.printf("%s alignments written (%.1f%%)\n", passed, 100.0 * passed / total);
    }
}

Example 24 with VDJCAlignments

use of com.milaboratory.mixcr.basictypes.VDJCAlignments in project mixcr by milaboratory.

the class ActionSortAlignments method go.

@Override
public void go(ActionHelper helper) throws Exception {
    try (VDJCAlignmentsReader reader = new VDJCAlignmentsReader(parameters.getInputFile())) {
        SmartProgressReporter.startProgressReport("Reading vdjca", reader);
        try (OutputPortCloseable<VDJCAlignments> sorted = Sorter.sort(reader, idComparator, 1024 * 512, new VDJCAlignmentsSerializer(reader), TempFileManager.getTempFile());
            VDJCAlignmentsWriter writer = new VDJCAlignmentsWriter(parameters.getOutputFile())) {
            writer.header(reader.getParameters(), reader.getUsedGenes());
            final long nReads = reader.getNumberOfReads();
            final CountingOutputPort<VDJCAlignments> counter = new CountingOutputPort<>(sorted);
            SmartProgressReporter.startProgressReport("Writing sorted alignments", SmartProgressReporter.extractProgress(counter, nReads));
            for (VDJCAlignments res : CUtils.it(counter)) writer.write(res);
            writer.setNumberOfProcessedReads(nReads);
        }
    }
}

Example 25 with VDJCAlignments

use of com.milaboratory.mixcr.basictypes.VDJCAlignments in project mixcr by milaboratory.

the class VDJCAlignerPVFirst method processPartial.

private VDJCAlignmentResult<PairedRead> processPartial(PairedRead input, PAlignmentHelper[] helpers) {
    // Calculates which PTarget was aligned with the highest score
    helpers[0].performCDAlignment();
    PAlignmentHelper bestHelper = helpers[0];
    for (int i = 1; i < helpers.length; ++i) {
        helpers[i].performCDAlignment();
        if (bestHelper.score() < helpers[i].score())
            bestHelper = helpers[i];
    }
    if (!bestHelper.hasVOrJHits()) {
        onFailedAlignment(input, VDJCAlignmentFailCause.NoHits);
        return new VDJCAlignmentResult<>(input);
    }
    // Calculates if this score is bigger then the threshold
    if (bestHelper.score() < parameters.getMinSumScore()) {
        onFailedAlignment(input, VDJCAlignmentFailCause.LowTotalScore);
        return new VDJCAlignmentResult<>(input);
    }
    // Finally filtering hits inside this helper to meet minSumScore and maxHits limits
    bestHelper.filterHits(parameters.getMinSumScore(), parameters.getMaxHits());
    // TODO do we really need this ?
    if (!bestHelper.hasVOrJHits()) {
        onFailedAlignment(input, VDJCAlignmentFailCause.LowTotalScore);
        return new VDJCAlignmentResult<>(input);
    }
    VDJCAlignments alignments = bestHelper.createResult(input.getId(), this, input);
    // Final check
    if (!parameters.getAllowNoCDR3PartAlignments()) {
        // CDR3 Begin / End
        boolean containCDR3Parts = false;
        final VDJCHit bestV = alignments.getBestHit(GeneType.Variable);
        final VDJCHit bestJ = alignments.getBestHit(GeneType.Joining);
        for (int i = 0; i < 2; i++) {
            if ((bestV != null && bestV.getAlignment(i) != null && bestV.getAlignment(i).getSequence1Range().getTo() >= bestV.getGene().getPartitioning().getRelativePosition(parameters.getFeatureToAlign(GeneType.Variable), reqPointL)) || (bestJ != null && bestJ.getAlignment(i) != null && bestJ.getAlignment(i).getSequence1Range().getFrom() <= bestJ.getGene().getPartitioning().getRelativePosition(parameters.getFeatureToAlign(GeneType.Joining), reqPointR))) {
                containCDR3Parts = true;
                break;
            }
        }
        if (!containCDR3Parts) {
            onFailedAlignment(input, VDJCAlignmentFailCause.NoCDR3Parts);
            return new VDJCAlignmentResult<>(input);
        }
    }
    // Read successfully aligned
    onSuccessfulAlignment(input, alignments);
    if (bestHelper.vChimera)
        onSegmentChimeraDetected(GeneType.Variable, input, alignments);
    if (bestHelper.jChimera)
        onSegmentChimeraDetected(GeneType.Joining, input, alignments);
    return new VDJCAlignmentResult<>(input, alignments);
}