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

Example 21 with GeneType

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

the class CloneAccumulator method accumulate.

public synchronized void accumulate(ClonalSequence data, VDJCAlignments alignment, boolean mapped) {
    if (!mapped) {
        // Core sequence accumulation
        coreCount += alignment.getNumberOfReads();
        // Accumulate information about V-D-J alignments only for strictly clustered reads
        // (only for core clonotypes members)
        float score;
        // Accumulate information about all genes
        for (GeneType geneType : GeneType.VJC_REFERENCE) {
            TObjectFloatHashMap<VDJCGeneId> geneScores = this.geneScores.get(geneType);
            VDJCHit[] hits = alignment.getHits(geneType);
            if (hits.length == 0)
                continue;
            if (geneScores == null)
                this.geneScores.put(geneType, geneScores = new TObjectFloatHashMap<>());
            for (VDJCHit hit : hits) {
                // Calculating sum of natural logarithms of scores
                score = hit.getScore();
                geneScores.adjustOrPutValue(hit.getGene().getId(), score, score);
            }
        }
        aggregator.aggregate(data.getConcatenated().getQuality());
    } else
        // Mapped sequence accumulation
        mappedCount += alignment.getNumberOfReads();
}

Example 22 with GeneType

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

the class PartialAlignmentsAssemblerTest method test2a.

@Test
public void test2a() throws Exception {
    RandomUtil.reseedThreadLocal(47);
    final InputTestData input = createTestData(47);
    final NucleotideSequence reference = input.reference;
    final EnumMap<GeneType, int[]> refPositions = input.refPositions;
    NucleotideSequence left1 = reference.getRange(refPositions.get(Diversity)[0] - 85, refPositions.get(Diversity)[0] + 10);
    final char[] chars = left1.toString().toCharArray();
    chars[3] = 'a';
    left1 = new NucleotideSequence(new String(chars));
    PairedRead[] data = { createPair(0, left1, reference.getRange(refPositions.get(Diversity)[1], refPositions.get(Diversity)[1] + 85).getReverseComplement()), createPair(1, reference.getRange(refPositions.get(Diversity)[0] - 135, refPositions.get(Diversity)[0] - 30), reference.getRange(refPositions.get(Diversity)[0] - 8, refPositions.get(Diversity)[0] + 85).getReverseComplement()) };
    final TestResult testResult = processData(data, input);
    for (VDJCAlignments al : testResult.assembled) {
        MiXCRTestUtils.printAlignment(al);
    // System.out.println(input.VJJunction);
    // System.out.println(al.getFeature(GeneFeature.VJJunction).getSequence());
    // Assert.assertTrue(input.VJJunction.toString().contains(al.getFeature(GeneFeature.VJJunction).getSequence().toString()));
    }
}

Example 23 with GeneType

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

the class PartialAlignmentsAssemblerTest method createTestData.

public static InputTestData createTestData(long seed) throws Exception {
    EnumMap<GeneType, String> geneNames = new EnumMap<GeneType, String>(GeneType.class) {

        {
            put(Variable, "TRBV20-1*00");
            put(Diversity, "TRBD2*00");
            put(Joining, "TRBJ2-6*00");
            put(Constant, "TRBC2*00");
        }
    };
    // config
    RandomGenerator rnd = RandomUtil.getThreadLocalRandom();
    rnd.setSeed(seed);
    final VDJCAlignerParameters defaultFeatures = VDJCParametersPresets.getByName("default");
    defaultFeatures.getVAlignerParameters().setGeneFeatureToAlign(VRegion);
    defaultFeatures.getDAlignerParameters().setGeneFeatureToAlign(DRegion);
    defaultFeatures.getJAlignerParameters().setGeneFeatureToAlign(JRegion);
    // used alleles
    EnumMap<GeneType, VDJCGene> genes = new EnumMap<>(GeneType.class);
    // germline parts of sequences
    EnumMap<GeneType, NucleotideSequence> germlineRegions = gtMap();
    // left, right cut of germline
    EnumMap<GeneType, int[]> germlineCuts = gtMap();
    // begin, end positions in assembled sequence
    EnumMap<GeneType, int[]> refPositions = gtMap();
    // single assembled sequence
    SequenceBuilder<NucleotideSequence> referenceBuilder = NucleotideSequence.ALPHABET.createBuilder();
    NucleotideSequence VDJunction = TestUtil.randomSequence(NucleotideSequence.ALPHABET, 3, 10);
    NucleotideSequence DJJunction = TestUtil.randomSequence(NucleotideSequence.ALPHABET, 3, 10);
    for (GeneType gt : GeneType.VDJC_REFERENCE) {
        VDJCGene gene = VDJCLibraryRegistry.getDefault().getLibrary("default", "hs").get(geneNames.get(gt));
        NucleotideSequence seq = gene.getFeature(defaultFeatures.getFeatureToAlign(gt));
        int[] cuts = null;
        switch(gt) {
            case Variable:
                cuts = new int[] { 0, rnd.nextInt(gene.getFeature(GermlineVCDR3Part).size() - 5) };
                break;
            case Diversity:
                cuts = new int[] { rnd.nextInt(seq.size() / 3), rnd.nextInt(seq.size() / 3) };
                break;
            case Joining:
                cuts = new int[] { rnd.nextInt(gene.getFeature(GermlineJCDR3Part).size() - 5), 0 };
                break;
            case Constant:
                cuts = new int[] { 0, rnd.nextInt(seq.size() / 2) };
                break;
        }
        NucleotideSequence gSeq = seq.getRange(cuts[0], seq.size() - cuts[1]);
        int[] positions = new int[2];
        positions[0] = referenceBuilder.size();
        referenceBuilder.append(gSeq);
        positions[1] = referenceBuilder.size();
        if (gt == Variable)
            referenceBuilder.append(VDJunction);
        if (gt == Diversity)
            referenceBuilder.append(DJJunction);
        genes.put(gt, gene);
        germlineCuts.put(gt, cuts);
        germlineRegions.put(gt, gSeq);
        refPositions.put(gt, positions);
    }
    NucleotideSequence VJJunction = NucleotideSequence.ALPHABET.createBuilder().append(VDJunction).append(germlineRegions.get(Diversity)).append(DJJunction).createAndDestroy();
    NucleotideSequence reference = referenceBuilder.createAndDestroy();
    return new InputTestData(genes, germlineRegions, germlineCuts, refPositions, VDJunction, DJJunction, reference, VJJunction);
}

Example 24 with GeneType

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

the class PartialAlignmentsAssemblerTest method test1.

// @Test
// public void testMaxAllele() throws Exception {
// final LociLibrary ll = LociLibraryManager.getDefault().getLibrary("mi");
// final Locus locus = Locus.TRB;
// 
// for (GeneFeature feature : new GeneFeature[]{VRegionWithP, DRegion, JRegionWithP, CRegion}) {
// Allele maxAllele = null;
// for (Allele allele : ll.getAllAlleles()) {
// if (allele.getLocusContainer().getSpeciesAndLocus().taxonId != Species.HomoSapiens)
// continue;
// if (!allele.isFunctional())
// continue;
// if (allele.getLocus() != locus)
// continue;
// if (maxAllele == null && allele.getFeature(feature) != null)
// maxAllele = allele;
// if (allele.getFeature(feature) != null && allele.getFeature(feature).size() > maxAllele.getFeature(feature).size())
// maxAllele = allele;
// }
// 
// System.out.println(maxAllele.getName() + "    Size: " + maxAllele.getFeature(feature).size());
// }
// }
@Test
public void test1() throws Exception {
    final InputTestData input = createTestData();
    final NucleotideSequence reference = input.reference;
    final EnumMap<GeneType, int[]> refPositions = input.refPositions;
    PairedRead[] data = { createPair(0, reference.getRange(refPositions.get(Variable)[1] - 85, refPositions.get(Variable)[1] + 15), reference.getRange(refPositions.get(Joining)[1] - 20, refPositions.get(Joining)[1] + 80).getReverseComplement()), createPair(1, reference.getRange(refPositions.get(Variable)[1] - 186, refPositions.get(Variable)[1] - 86), reference.getRange(refPositions.get(Variable)[1] - 10, refPositions.get(Variable)[1] + 102).getReverseComplement()) };
    final TestResult testResult = processData(data, input);
    for (VDJCAlignments al : testResult.assembled) {
        MiXCRTestUtils.printAlignment(al);
    }
}

Example 25 with GeneType

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

the class MiXCRTestUtils method assertAlignments.

public static void assertAlignments(VDJCAlignments alignments) {
    for (GeneType gt : GeneType.VDJC_REFERENCE) {
        for (VDJCHit hit : alignments.getHits(gt)) {
            for (int targetIndex = 0; targetIndex < alignments.numberOfTargets(); targetIndex++) {
                Alignment<NucleotideSequence> al = hit.getAlignment(targetIndex);
                if (al == null)
                    continue;
                NucleotideSequence sequence = alignments.getTarget(targetIndex).getSequence();
                AlignerTest.assertAlignment(al, sequence);
            }
        }
    }
}