Examples with GGene io.repseq.gen.GGene used on opensource projects

Example 1 with GGene

use of io.repseq.gen.GGene in project repseqio by repseqio.

the class MarkovInsertModel method create.

@Override
public InsertGenerator create(RandomGenerator random, final boolean v, List<VDJCGene> vGenes, List<VDJCGene> dGenes, List<VDJCGene> jGenes, List<VDJCGene> cGenes) {
    Map<Byte, List<Pair<Byte, Double>>> distParams = new HashMap<>();
    for (Map.Entry<String, Double> s : distribution.entrySet()) {
        String[] split = s.getKey().split(">");
        if (split.length != 2 || split[0].length() != 1 || split[1].length() != 1)
            throw new IllegalArgumentException("Illegal distribution key: " + s.getKey() + ". " + "Expected something like \"A>C\"");
        byte codeFrom = NucleotideSequence.ALPHABET.symbolToCode(split[0].charAt(0));
        byte codeTo = NucleotideSequence.ALPHABET.symbolToCode(split[1].charAt(0));
        if (codeFrom == -1 || codeTo == -1)
            throw new IllegalArgumentException("Illegal nucleotide in: " + s.getKey() + ".");
        List<Pair<Byte, Double>> pairs = distParams.get(codeFrom);
        if (pairs == null)
            distParams.put(codeFrom, pairs = new ArrayList<>());
        pairs.add(new Pair<>(codeTo, s.getValue()));
    }
    final Map<Byte, EnumeratedDistribution<Byte>> dists = new HashMap<>();
    for (byte from = 0; from < NucleotideSequence.ALPHABET.basicSize(); from++) {
        List<Pair<Byte, Double>> d = distParams.get(from);
        if (d == null)
            throw new IllegalArgumentException("No distribution for letter: " + NucleotideSequence.ALPHABET.codeToSymbol(from));
        dists.put(from, new EnumeratedDistribution<>(random, d));
    }
    final IndependentIntGenerator lengthDist = lengthDistribution.create(random);
    return new InsertGenerator() {

        @Override
        public NucleotideSequence generate(GGene gene) {
            ReferencePoint point = beginPoint(fromLeft, v);
            int pointPosition = gene.getPartitioning().getPosition(point);
            if (pointPosition == -1)
                throw new RuntimeException("Point " + point + " is not available for gene " + gene);
            byte letter = gene.getSequence(new Range(pointPosition, pointPosition + 1)).codeAt(0);
            int length = lengthDist.sample();
            byte[] array = new byte[length];
            for (int i = 0; i < length; i++) {
                byte cLetter = dists.get(letter).sample();
                array[i] = cLetter;
                letter = cLetter;
            }
            if (!fromLeft)
                ArraysUtils.reverse(array);
            return NucleotideSequence.ALPHABET.createBuilder().ensureCapacity(length).append(array).createAndDestroy();
        }
    };
}

Example 2 with GGene

use of io.repseq.gen.GGene in project repseqio by repseqio.

the class GenerateClonesAction method go.

@Override
public void go(ActionHelper helper) throws Exception {
    GCloneModel model = GModels.getGCloneModelByName(params.getModelName());
    GCloneGenerator generator = model.create(new Well19937c(params.getSeed()), VDJCLibraryRegistry.getDefault());
    VDJCLibrary library = VDJCLibraryRegistry.getDefault().getLibrary(model.libraryId());
    try (BufferedOutputStream s = new BufferedOutputStream(params.getOutput().equals(".") ? System.out : new FileOutputStream(params.getOutput()), 128 * 1024)) {
        s.write(GlobalObjectMappers.toOneLine(model.libraryId()).getBytes());
        s.write('\n');
        ObjectWriter writer = GlobalObjectMappers.ONE_LINE.writerFor(new TypeReference<GClone>() {
        }).withAttribute(VDJCGene.JSON_CURRENT_LIBRARY_ATTRIBUTE_KEY, library);
        OUTER: for (int i = 0; i < params.numberOfClones; i++) {
            GClone clone = generator.sample();
            for (GGene g : clone.genes.values()) {
                NucleotideSequence cdr3 = g.getFeature(GeneFeature.CDR3);
                if (params.isInFrame())
                    if (cdr3.size() % 3 != 0) {
                        --i;
                        continue OUTER;
                    }
                if (params.isNoStops())
                    if (AminoAcidSequence.translateFromCenter(cdr3).containStops()) {
                        --i;
                        continue OUTER;
                    }
            }
            writer.writeValue(new CloseShieldOutputStream(s), clone);
            s.write('\n');
        }
    }
}

Example 3 with GGene

use of io.repseq.gen.GGene in project repseqio by repseqio.

the class BasicGCloneModel method create.

@Override
public GCloneGenerator create(RandomGenerator random, VDJCLibraryRegistry registry) {
    VDJCLibrary library = registry.getLibrary(vdjcLibrary);
    final IndependentRealGenerator abundanceGenerator = abundanceModel.create(random);
    final Map<String, GGeneGenerator> geneGenerators = new HashMap<>();
    for (Map.Entry<String, GGeneModel> e : geneModels.entrySet()) geneGenerators.put(e.getKey(), e.getValue().create(random, library));
    return new GCloneGenerator() {

        @Override
        public GClone sample() {
            double abundance = abundanceGenerator.generate();
            Map<String, GGene> genes = new HashMap<>();
            for (Map.Entry<String, GGeneGenerator> e : geneGenerators.entrySet()) genes.put(e.getKey(), e.getValue().generate());
            return new GClone(abundance, genes);
        }
    };
}

Example 4 with GGene

use of io.repseq.gen.GGene in project repseqio by repseqio.

the class BasicGGeneModel method create.

@Override
public GGeneGenerator create(RandomGenerator random, VDJCLibrary library) {
    final VDJCGenesGenerator vdjcGenesGenerator = vdjcGenesModel.create(random, library);
    List<VDJCGene> vGenes = vdjcGenesGenerator.genes(GeneType.Variable);
    List<VDJCGene> dGenes = vdjcGenesGenerator.genes(GeneType.Diversity);
    List<VDJCGene> jGenes = vdjcGenesGenerator.genes(GeneType.Joining);
    List<VDJCGene> cGenes = vdjcGenesGenerator.genes(GeneType.Constant);
    final VDJTrimmingGenerator trimmingGenerator = trimmingModel.create(random, vGenes, dGenes, jGenes, cGenes);
    final InsertGenerator vInsertGenerator = vInsertModel.create(random, true, vGenes, dGenes, jGenes, cGenes);
    final InsertGenerator djInsertGenerator = dGenes.isEmpty() ? null : djInsertModel.create(random, false, vGenes, dGenes, jGenes, cGenes);
    return new GGeneGenerator() {

        @Override
        public GGene generate() {
            VDJCGenes vdjcGenes = vdjcGenesGenerator.sample();
            VDJTrimming trimming = trimmingGenerator.sample(vdjcGenes);
            assert !vdjcGenes.isDDefined() || (vdjcGenes.isDDefined() && djInsertGenerator != null);
            NucleotideSequence vInsert;
            NucleotideSequence djInsert;
            if (vdjcGenes.isDDefined()) {
                assert djInsertGenerator != null;
                GGene tempGene = new GGene(null, vdjcGenes, trimming, NucleotideSequence.EMPTY, NucleotideSequence.EMPTY);
                vInsert = vInsertGenerator.generate(tempGene);
                djInsert = djInsertGenerator.generate(tempGene);
            } else {
                GGene tempGene = new GGene(null, vdjcGenes, trimming, NucleotideSequence.EMPTY, null);
                vInsert = vInsertGenerator.generate(tempGene);
                djInsert = null;
            }
            return new GGene(null, vdjcGenes, trimming, vInsert, djInsert);
        }
    };
}

Example 5 with GGene

use of io.repseq.gen.GGene in project repseqio by repseqio.

the class BasicGCloneModelTest method test1.

@Test
public void test1() throws Exception {
    GGeneModel geneModel = new BasicGGeneModel(new IndependentVDJCGenesModel(b("TRBV12-2*00", 1.0).put("TRBV12-3*00", 0.0).get(), b("TRBD1*00", 1.0).put("TRBD2*00", 0.0).get(), b("TRBJ1-2*00", 1.0).put("TRBJ1-3*00", 0.0).get(), b("TRBC1*00", 1.0).put("TRBC2*00", 0.0).get()), new IndependentVDJTrimmingModel(new CommonCategoricalGeneTrimmingModel(b(-1, 1.0).get()), new CommonCategoricalDGeneTrimmingModel(b("-2|-3", 1.0).get()), new CommonCategoricalGeneTrimmingModel(b(-4, 1.0).get())), new FixedInsertModel(new NucleotideSequence("ATTA")), new FixedInsertModel(new NucleotideSequence("GACA")));
    BasicGCloneModel model = new BasicGCloneModel(new VDJCLibraryId("default", 9606), new FixedRealModel(1.0), b("TRB", geneModel).get());
    TestUtil.assertJson(model);
    GCloneGenerator gen = model.create(new Well19937c(123), VDJCLibraryRegistry.getDefault());
    GClone clone = gen.sample();
    TestUtil.assertJson(clone);
    GGene trb = clone.genes.get("TRB");
    assertEquals(trb.vdjcGenes.v.getName(), "TRBV12-2*00");
    assertEquals(trb.vdjcGenes.d.getName(), "TRBD1*00");
    assertEquals(trb.vdjcGenes.j.getName(), "TRBJ1-2*00");
    assertEquals(trb.vdjcGenes.c.getName(), "TRBC1*00");
    assertEquals(new VDJTrimming(-1, -4, -2, -3), trb.vdjTrimming);
    assertEquals(new NucleotideSequence("ATTA"), trb.vInsert);
    assertEquals(new NucleotideSequence("GACA"), trb.djInsert);
}