Examples with NucleotideSequence com.milaboratory.core.sequence.NucleotideSequence used on opensource projects

Example 11 with NucleotideSequence

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

the class TargetBuilderTest method testGenerate1.

@Test
public void testGenerate1() throws Exception {
    VDJCLibrary library = VDJCLibraryRegistry.getDefault().getLibrary("default", "hs");
    TargetBuilder.VDJCGenes genes = new TargetBuilder.VDJCGenes(library, "TRBV12-1*00", "TRBD1*00", "TRBJ1-3*00", "TRBC2*00");
    String model = "{CDR3Begin(-20)}VVVVVVVVVVVvVVVvVVVVVVVVVVVVVNNNNNNN{DBegin(0)}DDDDDDDDDDNN{CDR3End(-10)}JJJJJJJJJJJJJJJJJJJJ";
    NucleotideSequence nucleotideSequence = TargetBuilder.generateSequence(genes, model, new Well44497b());
    Assert.assertEquals(36 + 12 + 20, nucleotideSequence.size());
}

Example 12 with NucleotideSequence

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

the class VDJCObjectExtenderTest method testTripleRead.

@Test
public void testTripleRead() throws Exception {
    final boolean print = true;
    Well44497b rg = new Well44497b(12312);
    final VDJCAlignerParameters rnaSeqParams = VDJCParametersPresets.getByName("rna-seq");
    final PartialAlignmentsAssemblerAligner aligner = new PartialAlignmentsAssemblerAligner(rnaSeqParams);
    final 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");
    // | 310  | 338   | 438
    // 250V + 60CDR3 (20V 7N 10D 3N 20J) + 28J + 100C + 100N
    final NucleotideSequence baseSeq = TargetBuilder.generateSequence(genes, "{CDR3Begin(-250)}V*270 NNNNNNN {DBegin(0)}D*10 NNN {CDR3End(-20):FR4End} {CBegin}C*100 N*100", rg);
    F4 goAssert = new F4() {

        @Override
        public VDJCAlignments go(int len, int offset1, int offset2, int offset3) {
            NucleotideSequence seq1 = baseSeq.getRange(offset1, offset1 + len);
            NucleotideSequence seq2 = baseSeq.getRange(offset2, offset2 + len);
            NucleotideSequence seq3 = offset3 == -1 ? null : baseSeq.getRange(offset3, offset3 + len);
            VDJCAlignmentResult<VDJCMultiRead> alignment = offset3 == -1 ? aligner.process(MiXCRTestUtils.createMultiRead(seq1, seq2)) : aligner.process(MiXCRTestUtils.createMultiRead(seq1, seq2, seq3));
            VDJCAlignments al = alignment.alignment;
            Assert.assertNotNull(al);
            VDJCObjectExtender<VDJCAlignments> extender = new VDJCObjectExtender<>(Chains.TCR, (byte) 35, rnaSeqParams.getVAlignerParameters().getParameters().getScoring(), rnaSeqParams.getJAlignerParameters().getParameters().getScoring(), 100, 70, ReferencePoint.CDR3Begin, ReferencePoint.CDR3End);
            MiXCRTestUtils.assertAlignments(al);
            if (print) {
                MiXCRTestUtils.printAlignment(al);
                System.out.println();
                System.out.println("-------------------------------------------");
                System.out.println();
            }
            VDJCAlignments processed = extender.process(al);
            if (print) {
                MiXCRTestUtils.printAlignment(processed);
                System.out.println();
                System.out.println("===========================================");
                System.out.println();
                System.out.println();
            }
            MiXCRTestUtils.assertAlignments(processed);
            Assert.assertEquals(al.getFeature(GeneFeature.VDJunction), processed.getFeature(GeneFeature.VDJunction));
            Assert.assertEquals(al.getFeature(GeneFeature.DJJunction), processed.getFeature(GeneFeature.DJJunction));
            Assert.assertEquals(al.getFeature(GeneFeature.VJJunction), processed.getFeature(GeneFeature.VJJunction));
            return processed;
        }
    };
    VDJCAlignments a1 = goAssert.go(60, 245, 307, 450);
    Assert.assertEquals(2, a1.numberOfTargets());
    VDJCAlignments a2 = goAssert.go(60, 245, 315, 450);
    Assert.assertEquals(3, a2.numberOfTargets());
    VDJCAlignments a3 = goAssert.go(60, 245, 315, -1);
    Assert.assertEquals(2, a3.numberOfTargets());
    VDJCAlignments a4 = goAssert.go(60, 245, 307, -1);
    Assert.assertEquals(1, a4.numberOfTargets());
    VDJCAlignments a5 = goAssert.go(53, 252, 307, -1);
    Assert.assertEquals(1, a5.numberOfTargets());
    VDJCAlignments a6 = goAssert.go(53, 252, 307, 450);
    Assert.assertEquals(2, a6.numberOfTargets());
}

Example 13 with NucleotideSequence

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

the class VDJCAlignerPVFirstTest method test2.

@Test
@Ignore
public void test2() throws Exception {
    PairedRead read1 = new PairedRead(new SingleReadImpl(0, new NSequenceWithQuality(new NucleotideSequence("GCTGTGTATTACTGTGCAAGAGGGCCCCAAGAAAATAGTGGTTATTACTACGGGTTTGACTACTGGGGCCAGGGA"), SequenceQuality.GOOD_QUALITY_VALUE), "206"), new SingleReadImpl(0, new NSequenceWithQuality(new NucleotideSequence("GGCGCCAGGGGGAAGACCGATGGGCCCTTGGTGGAGGCTGAGGAGACGGTGACCAGGGTTCCCTGGCCCCAGTAG"), SequenceQuality.GOOD_QUALITY_VALUE), "206"));
    PairedRead read2 = new PairedRead(new SingleReadImpl(1, new NSequenceWithQuality(new NucleotideSequence("GCTGTGTATTACTGTGCAAGAGGGCCCCAAGAAAATAGTGGTTATTACTACGGGTTTGACTACTGGGGCCAGGGA"), SequenceQuality.GOOD_QUALITY_VALUE), "11621"), new SingleReadImpl(1, new NSequenceWithQuality(new NucleotideSequence("GGCGCCAGGGGGAAGACCGATGGGCCCTTGGTGGAGGCTGAGGAGACGGTGACCAGGGTTCCCTGGCCCCAGTAG"), SequenceQuality.GOOD_QUALITY_VALUE), "11621"));
    RunMiXCR.RunMiXCRAnalysis params = new RunMiXCR.RunMiXCRAnalysis(read1);
    RunMiXCR.AlignResult align = RunMiXCR.align(params);
    for (VDJCAlignments al : align.alignments) {
        for (int i = 0; i < al.numberOfTargets(); i++) {
            System.out.println(VDJCAlignmentsFormatter.getTargetAsMultiAlignment(al, i));
            System.out.println();
        }
        System.out.println();
        System.out.println(" ================================================ ");
        System.out.println();
    }
}

Example 14 with NucleotideSequence

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

the class VDJCAlignerSTest method test2.

@Test
@Ignore
public void test2() throws Exception {
    // @
    // GCTGTGTATTACTGTGCAAGAGGGCCCCAAGAAAATAGTGGTTATTACTACGGGTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAGCCTCCACCAAGGGCCCATCGGTCTTCCCCCTGGCGCC
    // +
    // CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
    VDJCAlignerParameters parameters = VDJCParametersPresets.getByName("default");
    VDJCAlignerS aligner = new VDJCAlignerS(parameters);
    for (VDJCGene gene : VDJCLibraryRegistry.getDefault().getLibrary("default", "hs").getGenes(Chains.IGH)) if (parameters.containsRequiredFeature(gene))
        aligner.addGene(gene);
    SingleReadImpl read = new SingleReadImpl(0, new NSequenceWithQuality(new NucleotideSequence("GCTGTGTATTACTGTGCAAGAGGGCCCCAAGAAAATAGTGGTTATTACTACGGGTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAGCCTCCACCAAGGGCCCATCGGTCTTCCCCCTGGCGCC"), SequenceQuality.GOOD_QUALITY_VALUE), "");
    RandomUtil.getThreadLocalRandom().setSeed(29);
    VDJCAlignmentResult<SingleRead> result = aligner.process0(read);
}

Example 15 with NucleotideSequence

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

the class AlignedTarget method orderTargets.

public static List<AlignedTarget> orderTargets(List<AlignedTarget> targets) {
    // Selecting best gene by total score
    final EnumMap<GeneType, VDJCGene> bestGenes = new EnumMap<>(GeneType.class);
    for (GeneType geneType : GeneType.VDJC_REFERENCE) {
        TObjectLongMap<VDJCGene> scores = new TObjectLongHashMap<>();
        for (AlignedTarget target : targets) {
            for (VDJCHit hit : target.getAlignments().getHits(geneType)) {
                Alignment<NucleotideSequence> alignment = hit.getAlignment(target.getTargetId());
                if (alignment != null)
                    scores.adjustOrPutValue(hit.getGene(), (long) alignment.getScore(), (long) alignment.getScore());
            }
        }
        VDJCGene bestGene = null;
        long bestScore = Long.MIN_VALUE;
        TObjectLongIterator<VDJCGene> it = scores.iterator();
        while (it.hasNext()) {
            it.advance();
            if (bestScore < it.value()) {
                bestScore = it.value();
                bestGene = it.key();
            }
        }
        if (bestGene != null)
            bestGenes.put(geneType, bestGene);
    }
    // Class to facilitate comparison between targets
    final class Wrapper implements Comparable<Wrapper> {

        final AlignedTarget target;

        final EnumMap<GeneType, Alignment<NucleotideSequence>> alignments = new EnumMap<>(GeneType.class);

        Wrapper(AlignedTarget target) {
            this.target = target;
            for (VDJCGene gene : bestGenes.values()) for (VDJCHit hit : target.getAlignments().getHits(gene.getGeneType())) if (hit.getGene() == gene) {
                Alignment<NucleotideSequence> alignment = hit.getAlignment(target.targetId);
                if (alignment != null) {
                    alignments.put(gene.getGeneType(), alignment);
                    break;
                }
            }
        }

        GeneType firstAlignedGeneType() {
            for (GeneType geneType : GeneType.VDJC_REFERENCE) if (alignments.containsKey(geneType))
                return geneType;
            return null;
        }

        @Override
        public int compareTo(Wrapper o) {
            GeneType thisFirstGene = firstAlignedGeneType();
            GeneType otherFirstGene = o.firstAlignedGeneType();
            int cmp = Byte.compare(thisFirstGene.getOrder(), otherFirstGene.getOrder());
            return cmp != 0 ? cmp : Integer.compare(alignments.get(thisFirstGene).getSequence1Range().getLower(), o.alignments.get(thisFirstGene).getSequence1Range().getLower());
        }
    }
    // Creating wrappers and sorting list
    List<Wrapper> wrappers = new ArrayList<>(targets.size());
    for (AlignedTarget target : targets) {
        Wrapper wrapper = new Wrapper(target);
        if (wrapper.firstAlignedGeneType() == null)
            continue;
        wrappers.add(wrapper);
    }
    Collections.sort(wrappers);
    // Creating result
    List<AlignedTarget> result = new ArrayList<>(wrappers.size());
    for (Wrapper wrapper : wrappers) result.add(wrapper.target);
    return result;
}