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

Example 36 with NucleotideSequence

use of com.milaboratory.core.sequence.NucleotideSequence 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 37 with NucleotideSequence

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

the class InferAnchorPointsAction method go.

public void go(GeneFeature geneFeature, String inputFile, String outputFile) throws Exception {
    VDJCLibraryRegistry.resetDefaultRegistry();
    VDJCLibraryRegistry reg = VDJCLibraryRegistry.getDefault();
    // Map of library names
    Map<String, String> libraryNameToAddress = new HashMap<>();
    // Registering reference library
    int i = 0;
    for (String refAddress : params.getReference()) {
        String name = REFERENCE_LIBRARY_PREFIX + (i++);
        reg.registerLibraries(refAddress, name);
        libraryNameToAddress.put(name, refAddress);
    }
    if (params.getReference().isEmpty()) {
        reg.loadAllLibraries("default");
        for (VDJCLibrary library : reg.getLoadedLibraries()) libraryNameToAddress.put(library.getName(), "built-in");
    }
    // Registering target library
    reg.registerLibraries(inputFile, TARGET_LIBRARY_NAME);
    // Compile gene filter
    Pattern namePattern = params.name == null ? null : Pattern.compile(params.name);
    List<VDJCLibrary> refLibraries = reg.getLoadedLibrariesByNamePattern(REFERENCE_LIBRARY_PATTERN);
    SimpleBatchAlignerParameters<AminoAcidSequence> aParams = new SimpleBatchAlignerParameters<>(5, 0.4f, params.getAbsoluteMinScore(geneFeature), true, AffineGapAlignmentScoring.getAminoAcidBLASTScoring(BLASTMatrix.BLOSUM62, -10, -1));
    SimpleBatchAligner<AminoAcidSequence, Ref> aligner = new SimpleBatchAligner<>(aParams);
    int dbSize = 0;
    for (VDJCLibrary lib : refLibraries) {
        for (VDJCGene gene : lib.getGenes()) {
            NucleotideSequence nSeq = gene.getFeature(geneFeature);
            if (nSeq == null)
                continue;
            ReferencePoint frameReference = GeneFeature.getFrameReference(geneFeature);
            ReferencePoints partitioning = gene.getPartitioning();
            if (frameReference == null)
                continue;
            int relativePosition = partitioning.getRelativePosition(geneFeature, frameReference);
            if (relativePosition < 0)
                continue;
            TranslationParameters frame = withIncompleteCodon(relativePosition);
            AminoAcidSequence aaSequence = AminoAcidSequence.translate(nSeq, frame);
            aligner.addReference(aaSequence, new Ref(gene, frame, nSeq.size()));
            ++dbSize;
        }
    }
    System.out.println("DB size: " + dbSize);
    System.out.println();
    // Checking that db is not empty
    if (dbSize == 0)
        throw new RuntimeException("No reference genes.");
    ArrayList<VDJCLibraryData> result = new ArrayList<>();
    ByteArrayOutputStream bos = new ByteArrayOutputStream();
    PrintStream bufferPS = new PrintStream(bos);
    // Iteration over target genes
    for (VDJCLibrary lib : reg.getLoadedLibrariesByName(TARGET_LIBRARY_NAME)) {
        ArrayList<VDJCGeneData> genes = new ArrayList<>();
        for (VDJCGene targetGene : lib.getGenes()) {
            bos.reset();
            PrintStream ps = params.outputOnlyModified() ? bufferPS : System.out;
            if (namePattern != null && !namePattern.matcher(targetGene.getName()).matches()) {
                if (!params.outputOnlyModified())
                    genes.add(targetGene.getData());
                continue;
            }
            ps.println("Processing: " + targetGene.getName() + " (" + (targetGene.isFunctional() ? "F" : "P") + ") " + targetGene.getChains());
            // Getting gene feature sequence from target gene
            NucleotideSequence nSeq = targetGene.getFeature(geneFeature);
            if (nSeq == null) {
                ps.println("Failed to extract " + GeneFeature.encode(geneFeature));
                ps.println("================");
                ps.println();
                if (!params.outputOnlyModified())
                    genes.add(targetGene.getData());
                continue;
            }
            // Alignment result
            AlignmentResult<AlignmentHit<AminoAcidSequence, Ref>> bestAResult = null;
            TranslationParameters bestFrame = null;
            // Searching for best alignment
            for (TranslationParameters frame : TRANSLATION_PARAMETERS) {
                AminoAcidSequence aaSeq = AminoAcidSequence.translate(nSeq, frame);
                AlignmentResult<AlignmentHit<AminoAcidSequence, Ref>> r = aligner.align(aaSeq);
                if (r != null && r.hasHits() && (bestAResult == null || bestAResult.getBestHit().getAlignment().getScore() < r.getBestHit().getAlignment().getScore())) {
                    bestAResult = r;
                    bestFrame = frame;
                }
            }
            if (bestFrame == null) {
                ps.println("No alignments found.");
                if (!params.outputOnlyModified())
                    genes.add(targetGene.getData());
                continue;
            }
            List<AlignmentHit<AminoAcidSequence, Ref>> hits = bestAResult.getHits();
            VDJCGeneData targetGeneData = targetGene.getData().clone();
            boolean anyPointChanged = false;
            for (int ai = 0; ai < hits.size(); ai++) {
                // Accumulate output
                ByteArrayOutputStream localBos = new ByteArrayOutputStream();
                PrintStream localPS = new PrintStream(localBos);
                Alignment<AminoAcidSequence> bestAlignment = hits.get(ai).getAlignment();
                Ref bestRef = hits.get(ai).getRecordPayload();
                VDJCGene bestReferenceGene = bestRef.gene;
                localPS.println("Aligned with " + bestReferenceGene.getName() + " from " + libraryNameToAddress.get(bestReferenceGene.getParentLibrary().getName()) + " ; Score = " + bestAlignment.getScore());
                AlignmentHelper alignmentHelper = bestAlignment.getAlignmentHelper();
                for (AlignmentHelper h : alignmentHelper.split(150)) localPS.println(h + "\n");
                ReferencePoints targetPartitioning = targetGene.getPartitioning();
                ReferencePoints referencePartitioning = bestReferenceGene.getPartitioning();
                for (GeneFeature.ReferenceRange range : geneFeature) for (ReferencePoint point : range.getIntermediatePoints()) {
                    localPS.print(point + ": ");
                    boolean isAvailable = targetPartitioning.isAvailable(point);
                    if (isAvailable) {
                        localPS.println("already set");
                    }
                    if (!referencePartitioning.isAvailable(point)) {
                        if (!isAvailable)
                            localPS.println("not set in reference gene");
                        continue;
                    }
                    int ntPositionInReference = referencePartitioning.getRelativePosition(geneFeature, point);
                    // Projecting position
                    AminoAcidSequence.AminoAcidSequencePosition aaPositionInReferece = AminoAcidSequence.convertNtPositionToAA(ntPositionInReference, bestRef.ntSeqLength, bestRef.frame);
                    if (aaPositionInReferece == null) {
                        if (!isAvailable)
                            localPS.println("failed to convert to aa position in ref");
                        continue;
                    }
                    int aaPositionInTarget = Alignment.aabs(bestAlignment.convertToSeq2Position(aaPositionInReferece.aminoAcidPosition));
                    if (aaPositionInTarget == -1) {
                        if (!isAvailable)
                            localPS.println("failed to project using alignment");
                        continue;
                    }
                    int ntPositionInTarget = AminoAcidSequence.convertAAPositionToNt(aaPositionInTarget, nSeq.size(), bestFrame);
                    if (ntPositionInTarget == -1) {
                        if (!isAvailable)
                            localPS.println("failed");
                        continue;
                    }
                    ntPositionInTarget += aaPositionInReferece.positionInTriplet;
                    ntPositionInTarget = targetPartitioning.getAbsolutePosition(geneFeature, ntPositionInTarget);
                    if (ntPositionInTarget == -1) {
                        if (!isAvailable)
                            localPS.println("failed");
                        continue;
                    }
                    if (isAvailable) {
                        int existingPosition = targetPartitioning.getPosition(point);
                        if (existingPosition != ntPositionInTarget) {
                            localPS.println("inferred position differs from existing value.  existing: " + existingPosition + ", inferred: " + ntPositionInTarget);
                        }
                        continue;
                    }
                    localPS.println(ntPositionInTarget);
                    targetGeneData.getAnchorPoints().put(point, (long) ntPositionInTarget);
                    anyPointChanged = true;
                }
                if (!anyPointChanged) {
                    if (!params.outputOnlyModified() && ai == 0)
                        ps.write(localBos.toByteArray());
                } else {
                    ps.write(localBos.toByteArray());
                    break;
                }
            }
            ps.println("================");
            ps.println();
            if (anyPointChanged && params.outputOnlyModified())
                System.out.write(bos.toByteArray());
            genes.add(targetGeneData);
        }
        result.add(new VDJCLibraryData(lib.getData(), genes));
    }
    VDJCDataUtils.writeToFile(result, outputFile, false);
}

Example 38 with NucleotideSequence

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

the class TsvAction method go.

@Override
public void go(ActionHelper helper) throws Exception {
    VDJCLibraryRegistry reg = VDJCLibraryRegistry.getDefault();
    if (!"default".equals(params.getInput()))
        reg.registerLibraries(params.getInput());
    else
        reg.loadAllLibraries("default");
    Pattern chainPattern = params.chain == null ? null : Pattern.compile(params.chain);
    Pattern namePattern = params.name == null ? null : Pattern.compile(params.name);
    Long taxonFilter = params.taxonId;
    if (taxonFilter == null && params.species != null)
        taxonFilter = reg.resolveSpecies(params.species);
    try (BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(params.getOutputStream(), StandardCharsets.UTF_8))) {
        writer.write("Gene\tChains\tFeature\tStart\tStop\tSource\tSequence\n");
        for (VDJCLibrary lib : reg.getLoadedLibraries()) {
            if (taxonFilter != null && taxonFilter != lib.getTaxonId())
                continue;
            for (VDJCGene gene : lib.getGenes()) {
                if (chainPattern != null) {
                    boolean y = false;
                    for (String s : gene.getChains()) if (y |= chainPattern.matcher(s).matches())
                        break;
                    if (!y)
                        continue;
                }
                if (namePattern != null && !namePattern.matcher(gene.getName()).matches())
                    continue;
                for (GeneFeatureWithOriginalName feature : params.features) {
                    GeneFeature geneFeature = feature.feature;
                    NucleotideSequence featureSequence = gene.getFeature(geneFeature);
                    if (featureSequence == null)
                        continue;
                    // Don't output start and end positions for composite gene features
                    Long start = geneFeature.isComposite() ? null : gene.getData().getAnchorPoints().get(geneFeature.getFirstPoint());
                    Long end = geneFeature.isComposite() ? null : gene.getData().getAnchorPoints().get(geneFeature.getLastPoint());
                    NucleotideSequence nSequence = gene.getFeature(geneFeature);
                    List<String> tokens = Arrays.asList(gene.getGeneName(), gene.getChains().toString(), feature.originalName, // (so essentially 1-based inclusive). Report both as 1-based.
                    (start == null ? "" : params.isOneBased() ? String.valueOf(start + 1) : String.valueOf(start)), (end == null ? "" : String.valueOf(end)), gene.getData().getBaseSequence().getOrigin().toString(), nSequence.toString());
                    String delim = "";
                    for (String t : tokens) {
                        writer.write(delim);
                        writer.write(t);
                        delim = "\t";
                    }
                    writer.write('\n');
                }
            }
        }
    }
}

Example 39 with NucleotideSequence

use of com.milaboratory.core.sequence.NucleotideSequence 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();
        }
    }
}

Example 40 with NucleotideSequence

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

the class FastaAction method go.

@Override
public void go(ActionHelper helper) throws Exception {
    GeneFeature geneFeature = params.getGeneFeature();
    VDJCLibraryRegistry reg = VDJCLibraryRegistry.getDefault();
    if (!"default".equals(params.getInput()))
        reg.registerLibraries(params.getInput());
    else
        reg.loadAllLibraries("default");
    Pattern chainPattern = params.chain == null ? null : Pattern.compile(params.chain);
    Pattern namePattern = params.name == null ? null : Pattern.compile(params.name);
    Long taxonFilter = params.taxonId;
    if (taxonFilter == null && params.species != null)
        taxonFilter = reg.resolveSpecies(params.species);
    try (FastaWriter<NucleotideSequence> writer = CLIUtils.createSingleFastaWriter(params.getOutput())) {
        for (VDJCLibrary lib : reg.getLoadedLibraries()) {
            if (taxonFilter != null && taxonFilter != lib.getTaxonId())
                continue;
            for (VDJCGene gene : lib.getGenes()) {
                if (chainPattern != null) {
                    boolean y = false;
                    for (String s : gene.getChains()) if (y |= chainPattern.matcher(s).matches())
                        break;
                    if (!y)
                        continue;
                }
                if (namePattern != null && !namePattern.matcher(gene.getName()).matches())
                    continue;
                NucleotideSequence featureSequence = gene.getFeature(geneFeature);
                if (featureSequence == null)
                    continue;
                writer.write(gene.getName() + "|" + (gene.isFunctional() ? "F" : "P") + "|taxonId=" + gene.getParentLibrary().getTaxonId(), featureSequence);
            }
        }
    }
}