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

Example 1 with ReferencePoint

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

the class ActionAlignmentsStat method go.

@Override
public void go(ActionHelper helper) throws Exception {
    long[] geneFeatureCounters = new long[targetFeatures.length];
    AlignmentInfoCollector[] collectors = new AlignmentInfoCollector[targetFeatures.length + targetReferencePoints.length];
    int i = 0;
    for (GeneFeature targetFeature : targetFeatures) collectors[i++] = new GeneFeatureCoverageCollector(targetFeature);
    for (ReferencePoint targetReferencePoint : targetReferencePoints) collectors[i++] = new ReferencePointCoverageCollector(targetReferencePoint, 40, 40);
    final Collector collector = new Collector(collectors);
    try (VDJCAlignmentsReader reader = new VDJCAlignmentsReader(actionParameters.getInputFileName());
        PrintStream output = actionParameters.getOutputFileName().equals("-") ? System.out : new PrintStream(new BufferedOutputStream(new FileOutputStream(actionParameters.getOutputFileName()), 32768))) {
        SmartProgressReporter.startProgressReport("Analysis", reader);
        CUtils.processAllInParallel(reader, collector, Math.min(4, Runtime.getRuntime().availableProcessors()));
        collector.end();
        if (output == System.out)
            output.println();
        collector.write(output);
    }
}

Example 2 with ReferencePoint

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

the class VDJCAlignmentsFormatter method pd.

private static PointToDraw pd(ReferencePoint rp, String marker, int additionalOffset, Filter<SequencePartitioning> activator) {
    int offset = marker.indexOf('>');
    if (offset >= 0)
        return new PointToDraw(rp.move(additionalOffset), marker, -1 - offset - additionalOffset, activator);
    offset = marker.indexOf('<');
    if (offset >= 0)
        return new PointToDraw(rp.move(additionalOffset), marker, -offset - additionalOffset, activator);
    return new PointToDraw(rp, marker, 0, activator);
}

Example 3 with ReferencePoint

use of io.repseq.core.ReferencePoint in project repseqio by repseqio.

the class VDJCGeneDataTest method testSerialization1.

@Test
public void testSerialization1() throws Exception {
    VDJCGeneData gene = new VDJCGeneData(new BaseSequence("embedded://testseq"), "TRBV1", GeneType.Variable, true, Chains.TRB, new TreeMap<String, SortedSet<String>>(), new TreeMap<ReferencePoint, Long>());
    gene.addMetaValue("key", "val");
    String s1 = GlobalObjectMappers.toOneLine(gene);
    JsonNode n1 = GlobalObjectMappers.ONE_LINE.readTree(s1);
    assertTrue(n1.get("meta").get("key").isValueNode());
    assertEquals(gene, GlobalObjectMappers.ONE_LINE.readValue(s1, VDJCGeneData.class));
    gene.addMetaValue("key", "val1");
    String s2 = GlobalObjectMappers.toOneLine(gene);
    JsonNode n2 = GlobalObjectMappers.ONE_LINE.readTree(s2);
    assertFalse(n2.get("meta").get("key").isValueNode());
    assertEquals(gene, GlobalObjectMappers.ONE_LINE.readValue(s2, VDJCGeneData.class));
}

Example 4 with ReferencePoint

use of io.repseq.core.ReferencePoint 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 5 with ReferencePoint

use of io.repseq.core.ReferencePoint in project repseqio by repseqio.

the class DebugAction method go.

@Override
public void go(ActionHelper helper) throws Exception {
    VDJCLibraryRegistry reg = VDJCLibraryRegistry.getDefault();
    reg.registerLibraries(params.getInput());
    Pattern namePattern = params.name == null ? null : Pattern.compile(params.name);
    GeneFeature cdr3FirstTriplet = new GeneFeature(ReferencePoint.CDR3Begin, 0, 3);
    GeneFeature cdr3LastTriplet = new GeneFeature(ReferencePoint.CDR3End, -3, 0);
    GeneFeature vIntronDonor = new GeneFeature(ReferencePoint.VIntronBegin, 0, 2);
    GeneFeature vIntronAcceptor = new GeneFeature(ReferencePoint.VIntronEnd, -2, 0);
    for (VDJCLibrary lib : reg.getLoadedLibraries()) {
        for (VDJCGene gene : lib.getGenes()) {
            if (namePattern != null && !namePattern.matcher(gene.getName()).matches())
                continue;
            // First generate list of warning messages
            List<String> warnings = new ArrayList<>();
            if (gene.isFunctional() || params.getCheckAll()) {
                NucleotideSequence l3;
                switch(gene.getGeneType()) {
                    case Variable:
                        // Flag AA residues flanking CDR3
                        l3 = gene.getFeature(cdr3FirstTriplet);
                        if (l3 == null)
                            warnings.add("Unable to find CDR3 start");
                        else if (l3.size() != 3)
                            warnings.add("Unable to translate sequence: " + gene.getName() + " / " + l3);
                        else if (AminoAcidSequence.translate(l3).codeAt(0) != AminoAcidAlphabet.C)
                            warnings.add("CDR3 does not start with C, was: " + l3.toString() + " / " + AminoAcidSequence.translate(l3).toString() + " / CDR3Begin: " + gene.getData().getAnchorPoints().get(ReferencePoint.CDR3Begin));
                        // Flag suspicious exon borders
                        // https://schneider.ncifcrf.gov/gallery/SequenceLogoSculpture.gif
                        NucleotideSequence vIntronDonorSeq = gene.getFeature(vIntronDonor);
                        if (vIntronDonorSeq != null && !vIntronDonorSeq.toString().equals("GT") && !vIntronDonorSeq.toString().equals("GC"))
                            warnings.add("Expected VIntron sequence to start with GT, was: " + vIntronDonorSeq.toString());
                        NucleotideSequence vIntronAcceptorSeq = gene.getFeature(vIntronAcceptor);
                        if (vIntronAcceptorSeq != null && !vIntronAcceptorSeq.toString().equals("AG"))
                            warnings.add("Expected VIntron sequence to end with AG, was: " + vIntronAcceptorSeq.toString());
                        ReferencePoints partitioning = gene.getPartitioning();
                        if (partitioning.isAvailable(GeneFeature.VTranscriptWithout5UTR)) {
                            // Iterating over all reading-frame bound anchor points of V gene
                            for (ReferencePoint anchorPoint : ReferencePoint.DefaultReferencePoints) {
                                if (anchorPoint.getGeneType() != GeneType.Variable || !anchorPoint.isTripletBoundary())
                                    continue;
                                // And checking that they are in the same frame as Start (L1Begin)
                                int relativePosition = partitioning.getRelativePosition(GeneFeature.VTranscriptWithout5UTR, anchorPoint);
                                if (// Point is defined
                                relativePosition >= 0 && relativePosition % 3 != 0)
                                    warnings.add("Expected " + anchorPoint + " to have position dividable by three inside VTranscriptWithout5UTR. " + "This may indicate an error in the L2 boundaries.");
                            }
                        }
                        break;
                    case Joining:
                        // Flag AA residues flanking CDR3
                        l3 = gene.getFeature(cdr3LastTriplet);
                        if (l3 == null)
                            warnings.add("Unable to find CDR3 end");
                        else if (l3.size() != 3)
                            warnings.add("Unable to translate sequence: " + gene.getName() + " / " + l3);
                        else if (AminoAcidSequence.translate(l3).codeAt(0) != AminoAcidAlphabet.W && AminoAcidSequence.translate(l3).codeAt(0) != AminoAcidAlphabet.F)
                            warnings.add("CDR3 does not end with W or F, was: " + l3.toString() + " / " + AminoAcidSequence.translate(l3).toString() + " / CDR3End: " + gene.getData().getAnchorPoints().get(ReferencePoint.CDR3End));
                        break;
                }
                for (GeneFeature geneFeature : aaGeneFeatures.get(gene.getGeneType())) {
                    AminoAcidSequence aaSequence = getAminoAcidSequence(gene, geneFeature, gene.getFeature(geneFeature));
                    if (aaSequence != null) {
                        // Flag if contains stop codon
                        if (aaSequence.numberOfStops() > 0)
                            warnings.add(GeneFeature.encode(geneFeature) + " contains a stop codon");
                    }
                }
            }
            if (params.getProblemOnly() && warnings.isEmpty())
                continue;
            System.out.println(gene.getName() + " (" + (gene.isFunctional() ? "F" : "P") + ") " + gene.getChains() + " : " + lib.getTaxonId());
            if (!warnings.isEmpty()) {
                System.out.println();
                System.out.println("WARNINGS: ");
                for (String warning : warnings) {
                    System.out.println(warning);
                }
                System.out.println();
            }
            for (GeneFeature geneFeature : geneFeatures.get(gene.getGeneType())) {
                System.out.println();
                System.out.println(GeneFeature.encode(geneFeature));
                NucleotideSequence nSequence = gene.getFeature(geneFeature);
                AminoAcidSequence aaSequence = getAminoAcidSequence(gene, geneFeature, nSequence);
                System.out.print("N:   ");
                if (nSequence == null)
                    System.out.println("Not Available");
                else
                    System.out.println(nSequence);
                if (GeneFeature.getFrameReference(geneFeature) != null) {
                    System.out.print("AA:  ");
                    if (aaSequence == null)
                        System.out.println("Not Available");
                    else
                        System.out.println(aaSequence);
                }
            }
            System.out.println("=========");
            System.out.println();
        }
    }
}