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

Example 26 with VDJCGene

use of io.repseq.core.VDJCGene 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 27 with VDJCGene

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

the class VDJCAlignerPVFirstTest method test1.

@Test
public void test1() throws Exception {
    VDJCAlignerParameters parameters = VDJCParametersPresets.getByName("default");
    ByteArrayOutputStream bos = new ByteArrayOutputStream();
    List<VDJCAlignments> alignemntsList = new ArrayList<>();
    int header;
    int total = 0;
    int leftHit = 0;
    try (PairedFastqReader reader = new PairedFastqReader(VDJCAlignerSTest.class.getClassLoader().getResourceAsStream("sequences/sample_IGH_R1.fastq"), VDJCAlignerSTest.class.getClassLoader().getResourceAsStream("sequences/sample_IGH_R2.fastq"), true)) {
        VDJCAlignerPVFirst aligner = new VDJCAlignerPVFirst(parameters);
        for (VDJCGene gene : VDJCLibraryRegistry.getDefault().getLibrary("default", "hs").getGenes(Chains.IGH)) {
            if (parameters.containsRequiredFeature(gene))
                aligner.addGene(gene);
        }
        for (PairedRead read : CUtils.it(reader)) {
            ++total;
            VDJCAlignmentResult<PairedRead> result = aligner.process(read);
            if (result.alignment != null) {
                alignemntsList.add(result.alignment);
                for (VDJCHit hit : result.alignment.getHits(GeneType.Variable)) if (hit.getAlignment(0) != null && hit.getAlignment(1) != null)
                    ++leftHit;
            }
        }
    }
    System.out.println(alignemntsList.size());
    System.out.println(total);
    System.out.println(leftHit);
    Assert.assertTrue(alignemntsList.size() > 10);
    int k = 10;
    for (VDJCAlignments alignments : alignemntsList) {
        for (int target = 0; target < alignments.numberOfTargets(); target++) {
            MultiAlignmentHelper helperBig = VDJCAlignmentsFormatter.getTargetAsMultiAlignment(alignments, target);
            if (helperBig == null)
                continue;
            for (MultiAlignmentHelper helper : helperBig.split(80)) {
                System.out.println(helper);
                System.out.println();
                if (--k < 0)
                    return;
            }
        }
    }
// System.out.println("Bytes per alignment: " + (bos.size() - header) / alignemntsList.size());
// 
// try (VDJCAlignmentsReader reader = new VDJCAlignmentsReader(new ByteArrayInputStream(bos.toByteArray()), ll)) {
// int i = 0;
// for (VDJCAlignments alignments : CUtils.it(reader))
// Assert.assertEquals(alignemntsList.get(i++), alignments);
// }
}