Examples with AnnPredictionParserFactory com.github.lindenb.jvarkit.util.vcf.predictions.AnnPredictionParserFactory used on opensource projects

Example 1 with AnnPredictionParserFactory

use of com.github.lindenb.jvarkit.util.vcf.predictions.AnnPredictionParserFactory in project jvarkit by lindenb.

the class VcfBurdenFilterGenes method doVcfToVcf.

@Override
protected int doVcfToVcf(final String inputName, final VcfIterator in, final VariantContextWriter out) {
    final VCFHeader header = in.getHeader();
    try {
        final VCFHeader h2 = addMetaData(new VCFHeader(header));
        final VCFFilterHeaderLine filterControlsHeader;
        if (!StringUtil.isBlank(this.filterTag)) {
            filterControlsHeader = new VCFFilterHeaderLine(this.filterTag.trim(), "Genes not in list " + this.geneFile);
            h2.addMetaDataLine(filterControlsHeader);
        } else {
            filterControlsHeader = null;
        }
        final List<String> lookColumns = Arrays.asList("CCDS", "Feature", "ENSP", "Gene", "HGNC", "HGNC_ID", "SYMBOL", "RefSeq");
        final VepPredictionParser vepParser = new VepPredictionParserFactory(header).get();
        final AnnPredictionParser annParser = new AnnPredictionParserFactory(header).get();
        final SAMSequenceDictionaryProgress progess = new SAMSequenceDictionaryProgress(header.getSequenceDictionary()).logger(LOG);
        out.writeHeader(h2);
        while (in.hasNext() && !out.checkError()) {
            final VariantContext ctx = progess.watch(in.next());
            boolean keep = false;
            final VariantContextBuilder vcb = new VariantContextBuilder(ctx);
            // not just set FILTER ?
            if (filterControlsHeader == null) {
                vcb.rmAttribute(vepParser.getTag());
                vcb.rmAttribute(annParser.getTag());
            }
            final List<String> newVepList = new ArrayList<>();
            for (final String predStr : ctx.getAttributeAsList(vepParser.getTag()).stream().map(O -> String.class.cast(O)).collect(Collectors.toList())) {
                final VepPredictionParser.VepPrediction pred = vepParser.parseOnePrediction(ctx, predStr);
                for (final String col : lookColumns) {
                    final String token = pred.getByCol(col);
                    if (!StringUtil.isBlank(token) && this.geneNames.contains(token)) {
                        newVepList.add(predStr);
                        keep = true;
                        break;
                    }
                }
            }
            final List<String> newEffList = new ArrayList<>();
            for (final String predStr : ctx.getAttributeAsList(annParser.getTag()).stream().map(O -> String.class.cast(O)).collect(Collectors.toList())) {
                final AnnPredictionParser.AnnPrediction pred = annParser.parseOnePrediction(predStr);
                final String token = pred.getGeneName();
                if (!StringUtil.isBlank(token) && this.geneNames.contains(token)) {
                    newEffList.add(predStr);
                    keep = true;
                    break;
                }
            }
            // not just set FILTER ?
            if (filterControlsHeader == null) {
                if (!newVepList.isEmpty())
                    vcb.attribute(vepParser.getTag(), newVepList);
                if (!newEffList.isEmpty())
                    vcb.attribute(annParser.getTag(), newEffList);
            }
            if (filterControlsHeader != null) {
                if (!keep) {
                    vcb.filter(filterControlsHeader.getID());
                } else if (!ctx.isFiltered()) {
                    vcb.passFilters();
                }
                out.add(vcb.make());
            } else {
                if (keep)
                    out.add(vcb.make());
            }
        }
        progess.finish();
        return RETURN_OK;
    } catch (final Exception err) {
        LOG.error(err);
        return -1;
    } finally {
        CloserUtil.close(in);
    }
}

Example 2 with AnnPredictionParserFactory

use of com.github.lindenb.jvarkit.util.vcf.predictions.AnnPredictionParserFactory in project jvarkit by lindenb.

the class VcfTools method init.

public void init(final VCFHeader header) {
    this.header = header;
    this.snpEffPredictionParser = new SnpEffPredictionParserFactory().header(header).get();
    this.vepPredictionParser = new VepPredictionParserFactory().header(header).get();
    this.annPredictionParser = new AnnPredictionParserFactory(header).get();
}

Example 3 with AnnPredictionParserFactory

use of com.github.lindenb.jvarkit.util.vcf.predictions.AnnPredictionParserFactory in project jvarkit by lindenb.

the class AbstractGroupBy method initialize.

@Override
public void initialize() {
    final VCFHeader vcfHeader = GATKVCFUtils.getVCFHeadersFromRods(getToolkit()).get(variants.getName());
    this.annParser = new AnnPredictionParserFactory(vcfHeader).get();
    super.initialize();
}

Example 4 with AnnPredictionParserFactory

use of com.github.lindenb.jvarkit.util.vcf.predictions.AnnPredictionParserFactory in project jvarkit by lindenb.

the class VCFCompare method doWork.

@Override
public int doWork(final List<String> args) {
    if (args.isEmpty()) {
        LOG.error("VCFs missing.");
        return -1;
    }
    if (args.size() != 2) {
        System.err.println("Illegal number or arguments. Expected two VCFs");
        return -1;
    }
    PrintWriter pw = null;
    XMLStreamWriter w = null;
    InputStream in = null;
    SortingCollection<LineAndFile> variants = null;
    try {
        LineAndFileComparator varcmp = new LineAndFileComparator();
        variants = SortingCollection.newInstance(LineAndFile.class, new LineAndFileCodec(), varcmp, this.writingSortingCollection.getMaxRecordsInRam(), this.writingSortingCollection.getTmpPaths());
        variants.setDestructiveIteration(true);
        for (int i = 0; i < 2; ++i) {
            this.inputs[i] = new Input();
            this.inputs[i].codec = VCFUtils.createDefaultVCFCodec();
            this.inputs[i].filename = args.get(i);
            LOG.info("Opening " + this.inputs[i].filename);
            in = IOUtils.openURIForReading(this.inputs[i].filename);
            final LineReader lr = new SynchronousLineReader(in);
            final LineIterator li = new LineIteratorImpl(lr);
            this.inputs[i].header = (VCFHeader) this.inputs[i].codec.readActualHeader(li);
            this.inputs[i].vepPredictionParser = new VepPredictionParserFactory(this.inputs[i].header).get();
            this.inputs[i].snpEffPredictionParser = new SnpEffPredictionParserFactory(this.inputs[i].header).get();
            this.inputs[i].annPredictionParser = new AnnPredictionParserFactory(this.inputs[i].header).get();
            while (li.hasNext()) {
                LineAndFile laf = new LineAndFile();
                laf.fileIdx = i;
                laf.line = li.next();
                variants.add(laf);
            }
            LOG.info("Done Reading " + this.inputs[i].filename);
            CloserUtil.close(li);
            CloserUtil.close(lr);
            CloserUtil.close(in);
        }
        variants.doneAdding();
        LOG.info("Done Adding");
        Set<String> commonSamples = new TreeSet<String>(this.inputs[0].header.getSampleNamesInOrder());
        commonSamples.retainAll(this.inputs[1].header.getSampleNamesInOrder());
        List<Venn0> venn1List = new ArrayList<VCFCompare.Venn0>();
        venn1List.add(new Venn1("ALL"));
        venn1List.add(new Venn1("having ID") {

            @Override
            public VariantContext filter(VariantContext ctx, int fileIndex) {
                return ctx == null || !ctx.hasID() ? null : ctx;
            }
        });
        venn1List.add(new Venn1("QUAL greater 30") {

            @Override
            public VariantContext filter(VariantContext ctx, int fileIndex) {
                return ctx == null || !ctx.hasLog10PError() || ctx.getPhredScaledQual() < 30.0 ? null : ctx;
            }
        });
        for (VariantContext.Type t : VariantContext.Type.values()) {
            venn1List.add(new VennType(t));
        }
        for (SequenceOntologyTree.Term term : SequenceOntologyTree.getInstance().getTerms()) {
            venn1List.add(new VennPred("vep", term) {

                @Override
                Set<Term> terms(VariantContext ctx, int file_id) {
                    Set<Term> tt = new HashSet<SequenceOntologyTree.Term>();
                    for (VepPredictionParser.VepPrediction pred : VCFCompare.this.inputs[file_id].vepPredictionParser.getPredictions(ctx)) {
                        tt.addAll(pred.getSOTerms());
                    }
                    return tt;
                }
            });
            venn1List.add(new VennPred("SnpEff", term) {

                @Override
                Set<Term> terms(VariantContext ctx, int file_id) {
                    Set<Term> tt = new HashSet<SequenceOntologyTree.Term>();
                    for (SnpEffPredictionParser.SnpEffPrediction pred : VCFCompare.this.inputs[file_id].snpEffPredictionParser.getPredictions(ctx)) {
                        tt.addAll(pred.getSOTerms());
                    }
                    return tt;
                }
            });
            venn1List.add(new VennPred("ANN", term) {

                @Override
                Set<Term> terms(VariantContext ctx, int file_id) {
                    Set<Term> tt = new HashSet<SequenceOntologyTree.Term>();
                    for (AnnPredictionParser.AnnPrediction pred : VCFCompare.this.inputs[file_id].annPredictionParser.getPredictions(ctx)) {
                        tt.addAll(pred.getSOTerms());
                    }
                    return tt;
                }
            });
        }
        for (String s : commonSamples) {
            venn1List.add(new VennGType(s));
        }
        /* START : digest results ====================== */
        Counter<String> diff = new Counter<String>();
        List<LineAndFile> row = new ArrayList<LineAndFile>();
        CloseableIterator<LineAndFile> iter = variants.iterator();
        for (; ; ) {
            LineAndFile rec = null;
            if (iter.hasNext()) {
                rec = iter.next();
            }
            if (rec == null || (!row.isEmpty() && varcmp.compare(row.get(0), rec) != 0)) {
                if (!row.isEmpty()) {
                    diff.incr("count.variations");
                    VariantContext[] contexes_init = new VariantContext[] { null, null };
                    for (LineAndFile var : row) {
                        if (contexes_init[var.fileIdx] != null) {
                            LOG.error("Duplicate context in " + inputs[var.fileIdx].filename + " : " + var.line);
                            continue;
                        }
                        contexes_init[var.fileIdx] = var.getContext();
                    }
                    for (Venn0 venn : venn1List) {
                        venn.visit(contexes_init);
                    }
                    row.clear();
                }
                if (rec == null)
                    break;
            }
            row.add(rec);
        }
        iter.close();
        /* END : digest results ====================== */
        pw = super.openFileOrStdoutAsPrintWriter(outputFile);
        XMLOutputFactory xmlfactory = XMLOutputFactory.newInstance();
        w = xmlfactory.createXMLStreamWriter(pw);
        w.writeStartElement("html");
        w.writeStartElement("body");
        /* specific samples */
        w.writeStartElement("div");
        w.writeStartElement("dl");
        for (int i = 0; i < 3; ++i) {
            String title;
            Set<String> samples;
            switch(i) {
                case 0:
                case 1:
                    title = "Sample(s) for " + this.inputs[i].filename + ".";
                    samples = new TreeSet<String>(this.inputs[i].header.getSampleNamesInOrder());
                    samples.removeAll(commonSamples);
                    break;
                default:
                    title = "Common Sample(s).";
                    samples = new TreeSet<String>(commonSamples);
                    break;
            }
            w.writeStartElement("dt");
            w.writeCharacters(title);
            w.writeEndElement();
            w.writeStartElement("dd");
            w.writeStartElement("ol");
            for (String s : samples) {
                w.writeStartElement("li");
                w.writeCharacters(s);
                w.writeEndElement();
            }
            w.writeEndElement();
            w.writeEndElement();
        }
        // dl
        w.writeEndElement();
        // div
        w.writeEndElement();
        for (Venn0 v : venn1List) {
            v.write(w);
        }
        // body
        w.writeEndElement();
        // html
        w.writeEndElement();
        w.writeEndDocument();
        w.close();
        w = null;
        pw.flush();
        pw.close();
        pw = null;
    } catch (Exception err) {
        LOG.error(err);
        return -1;
    } finally {
        CloserUtil.close(w);
        CloserUtil.close(pw);
        if (variants != null)
            variants.cleanup();
    }
    return 0;
}

Example 5 with AnnPredictionParserFactory

use of com.github.lindenb.jvarkit.util.vcf.predictions.AnnPredictionParserFactory in project jvarkit by lindenb.

the class VCFComposite method doWork.

@Override
public int doWork(final List<String> args) {
    PrintWriter out = null;
    try {
        out = super.openFileOrStdoutAsPrintWriter(this.outputFile);
        if (listModels) {
            for (final Type t : Type.values()) {
                out.println(t.name());
                out.println("\t" + t.getDescription());
            }
            out.flush();
            return 0;
        }
        this.pedigree = Pedigree.newParser().parse(pedigreeFile);
        if (this.pedigree.getAffected().isEmpty()) {
            LOG.error("No Affected sample in " + this.pedigreeFile);
            return -1;
        }
        if (this.pedigree.getUnaffected().isEmpty()) {
            LOG.error("No Unaffected sample in " + this.pedigreeFile);
            return -1;
        }
        final DiseaseModel model = this.createModel();
        final String inputName = super.oneFileOrNull(args);
        final LineIterator r = (inputName == null ? IOUtils.openStreamForLineIterator(stdin()) : IOUtils.openURIForLineIterator(inputName));
        final VCFCodec codec = new VCFCodec();
        final VCFHeader header = (VCFHeader) codec.readActualHeader(r);
        final AnnPredictionParser annParser = new AnnPredictionParserFactory(header).get();
        final VepPredictionParser vepParser = new VepPredictionParserFactory(header).get();
        // final VCFHeader h2=new VCFHeader(header.getMetaDataInInputOrder(),header.getSampleNamesInOrder());
        // h2.addMetaDataLine(new VCFInfoHeaderLine(this.TAG,1,VCFHeaderLineType.String,"Values from bigwig file: "+BIGWIG));
        SortingCollection<GeneAndVariant> sorting = null;
        String prevContig = null;
        for (; ; ) {
            String line;
            final VariantContext ctx;
            if (r.hasNext()) {
                line = r.next();
                ctx = codec.decode(line);
            } else {
                line = null;
                ctx = null;
            }
            if (ctx == null || !ctx.getContig().equals(prevContig)) {
                if (sorting != null) {
                    LOG.debug("Dump contig " + prevContig);
                    sorting.doneAdding();
                    CloseableIterator<GeneAndVariant> iter2 = sorting.iterator();
                    EqualRangeIterator<GeneAndVariant> eqiter = new EqualRangeIterator<>(iter2, (A, B) -> A.gene.compareTo(B.gene));
                    while (eqiter.hasNext()) {
                        final List<GeneAndVariant> variants = eqiter.next();
                        model.scan(variants.get(0).gene, variants.stream().map(L -> codec.decode(L.ctxLine)).collect(Collectors.toList()), out);
                    }
                    eqiter.close();
                    iter2.close();
                    sorting.cleanup();
                }
                sorting = null;
                if (ctx == null)
                    break;
                prevContig = ctx.getContig();
            }
            if (!ctx.isVariant())
                continue;
            if (!acceptFiltered && ctx.isFiltered())
                continue;
            if (!acceptID && ctx.hasID())
                continue;
            if (!model.accept(ctx))
                continue;
            final Set<String> geneKeys = new HashSet<>();
            for (final AnnPredictionParser.AnnPrediction pred : annParser.getPredictions(ctx)) {
                geneKeys.addAll(pred.getGeneKeys().stream().map(S -> ctx.getContig() + "_" + S).collect(Collectors.toSet()));
            }
            for (final VepPredictionParser.VepPrediction pred : vepParser.getPredictions(ctx)) {
                geneKeys.addAll(pred.getGeneKeys().stream().map(S -> ctx.getContig() + "_" + S).collect(Collectors.toSet()));
            }
            if (sorting == null) {
                sorting = SortingCollection.newInstance(GeneAndVariant.class, new GeneAndVariantCodec(), (A, B) -> {
                    int i = A.gene.compareTo(B.gene);
                    if (i != 0)
                        return i;
                    return A.ctxLine.compareTo(B.ctxLine);
                }, this.writingSortingCollection.getMaxRecordsInRam(), this.writingSortingCollection.getTmpPaths());
                sorting.setDestructiveIteration(true);
            }
            for (final String gk : geneKeys) {
                final GeneAndVariant gav = new GeneAndVariant();
                gav.gene = gk;
                gav.ctxLine = line;
                sorting.add(gav);
            }
        }
        out.flush();
        out.close();
        out = null;
        return 0;
    } catch (Exception err) {
        LOG.error(err);
        return -1;
    } finally {
        CloserUtil.close(out);
    }
}