Examples with Gene com.github.lindenb.jvarkit.util.bio.structure.Gene used on opensource projects

Example 6 with Gene

use of com.github.lindenb.jvarkit.util.bio.structure.Gene in project jvarkit by lindenb.

the class VcfBurdenGtf method runBurden.

@Override
protected void runBurden(PrintWriter pw, VCFReader vcfReader, VariantContextWriter vcw) throws IOException {
    final SAMSequenceDictionary vcfDict = SequenceDictionaryUtils.extractRequired(vcfReader.getHeader());
    final List<Gene> all_genes;
    try (GtfReader gtfReader = new GtfReader(this.gtfFile)) {
        gtfReader.setContigNameConverter(ContigNameConverter.fromOneDictionary(vcfDict));
        all_genes = gtfReader.getAllGenes().stream().filter(G -> StringUtil.isBlank(this.intergenic_contig) || this.intergenic_contig.equals("*") || this.intergenic_contig.equals(G.getContig())).sorted(new ContigDictComparator(vcfDict).createLocatableComparator()).collect(Collectors.toCollection(ArrayList::new));
    }
    pw.print("#chrom");
    pw.print("\t");
    pw.print("start0");
    pw.print("\t");
    pw.print("end");
    pw.print("\t");
    pw.print("name");
    pw.print("\t");
    pw.print("length");
    pw.print("\t");
    pw.print("gene");
    pw.print("\t");
    pw.print("type");
    pw.print("\t");
    pw.print("strand");
    pw.print("\t");
    pw.print("transcript");
    pw.print("\t");
    pw.print("gene-id");
    pw.print("\t");
    pw.print("intervals");
    pw.print("\t");
    pw.print("p-value");
    pw.print("\t");
    pw.print("affected_alt");
    pw.print("\t");
    pw.print("affected_hom");
    pw.print("\t");
    pw.print("unaffected_alt");
    pw.print("\t");
    pw.print("unaffected_hom");
    pw.print("\t");
    pw.print("variants.count");
    pw.println();
    final List<SimpleInterval> all_intergenic = new ArrayList<>();
    if (!StringUtil.isBlank(this.intergenic_contig)) {
        for (final SAMSequenceRecord ssr : vcfDict.getSequences()) {
            if (!(this.intergenic_contig.equals("*") || this.intergenic_contig.equals(ssr.getSequenceName())))
                continue;
            final BitSet filled = new BitSet(ssr.getSequenceLength() + 2);
            all_genes.stream().filter(G -> G.getContig().equals(ssr.getSequenceName())).forEach(G -> filled.set(G.getStart(), 1 + /* bit set is 0 based */
            Math.min(G.getEnd(), ssr.getSequenceLength())));
            int i = 1;
            while (i < ssr.getSequenceLength()) {
                if (filled.get(i)) {
                    i++;
                    continue;
                }
                int j = i;
                while (j < ssr.getSequenceLength() && !filled.get(j)) {
                    j++;
                }
                all_intergenic.add(new SimpleInterval(ssr.getSequenceName(), i, j));
                i = j + 1;
            }
            all_genes.removeIf(G -> G.getContig().equals(ssr.getSequenceName()));
        }
        all_genes.clear();
    }
    final ProgressFactory.Watcher<Gene> progress = ProgressFactory.newInstance().logger(LOG).dictionary(vcfDict).build();
    /* run genes */
    for (final Gene gene : all_genes) {
        progress.apply(gene);
        final IntervalTree<VariantContext> intervalTree = new IntervalTree<>();
        vcfReader.query(gene).stream().filter(V -> accept(V)).forEach(V -> intervalTree.put(V.getStart(), V.getEnd(), V));
        if (intervalTree.size() == 0)
            continue;
        for (final Transcript transcript : gene.getTranscripts()) {
            final List<SubPartOfTranscript> parts = new ArrayList<>();
            parts.addAll(transcript.getExons().stream().map(R -> new SubPartOfTranscript(R)).collect(Collectors.toList()));
            parts.addAll(transcript.getIntrons().stream().map(R -> new SubPartOfTranscript(R)).collect(Collectors.toList()));
            final int intron_window_size = 1000;
            final int intron_window_shift = 500;
            for (final Intron intron : transcript.getIntrons()) {
                if (intron.getLengthOnReference() <= intron_window_size)
                    continue;
                int start_pos = intron.getStart();
                while (start_pos + intron_window_size <= intron.getEnd()) {
                    int xend = Math.min(intron.getEnd(), start_pos + intron_window_size - 1);
                    int xstart = xend - intron_window_size - 1;
                    parts.add(new SubPartOfTranscript(transcript, intron.getName() + ".Sliding", Collections.singletonList(new SimpleInterval(intron.getContig(), xstart, xend))));
                    start_pos += intron_window_shift;
                }
            }
            for (final UTR utr : transcript.getUTRs()) {
                parts.add(new SubPartOfTranscript(transcript, utr.getName(), utr.getIntervals()));
            }
            if (transcript.getExonCount() > 1) {
                parts.add(new SubPartOfTranscript(transcript, "AllExons", transcript.getExons().stream().map(E -> E.toInterval()).collect(Collectors.toList())));
            }
            if (transcript.hasCodonStartDefined() && transcript.hasCodonStopDefined() && transcript.getAllCds().size() > 1) {
                parts.add(new SubPartOfTranscript(transcript, "AllCds", transcript.getAllCds().stream().map(E -> E.toInterval()).collect(Collectors.toList())));
            }
            final int L = transcript.getTranscriptLength();
            final int[] index2genomic = new int[L];
            int pos = 0;
            for (final Exon exon : transcript.getExons()) {
                for (int i = exon.getStart(); i <= exon.getEnd(); i++) {
                    index2genomic[pos] = i;
                    pos++;
                }
            }
            final int window_size = 200;
            final int window_shift = 100;
            int array_index = 0;
            while (array_index < index2genomic.length) {
                final List<Locatable> intervals = new ArrayList<>();
                int prev_pos = -1;
                int start_pos = index2genomic[array_index];
                int i = 0;
                while (i < window_size && array_index + i < index2genomic.length) {
                    final int curr_pos = index2genomic[array_index + i];
                    if (i > 0 && prev_pos + 1 != curr_pos) {
                        intervals.add(new SimpleInterval(transcript.getContig(), start_pos, prev_pos));
                        start_pos = curr_pos;
                    }
                    prev_pos = curr_pos;
                    i++;
                }
                intervals.add(new SimpleInterval(transcript.getContig(), start_pos, prev_pos));
                parts.add(new SubPartOfTranscript(transcript, "Sliding", intervals));
                array_index += window_shift;
            }
            for (final SubPartOfTranscript part : parts) {
                final List<VariantContext> variants = new ArrayList<>();
                for (final Locatable loc : part.intervals) {
                    Iterator<IntervalTree.Node<VariantContext>> iter = intervalTree.overlappers(loc.getStart(), loc.getEnd());
                    while (iter.hasNext()) variants.add(iter.next().getValue());
                }
                if (variants.isEmpty())
                    continue;
                final FisherResult fisher = runFisher(variants);
                if (fisher.p_value > this.fisherTreshold)
                    continue;
                if (vcw != null) {
                    for (final VariantContext ctx : variants) {
                        vcw.add(new VariantContextBuilder(ctx).attribute(BURDEN_KEY, VCFUtils.escapeInfoField(part.label)).make());
                    }
                }
                pw.print(part.getContig());
                pw.print("\t");
                pw.print(part.getStart() - 1);
                pw.print("\t");
                pw.print(part.getEnd());
                pw.print("\t");
                pw.print(part.label);
                pw.print("\t");
                pw.print(part.getLengthOnReference());
                pw.print("\t");
                pw.print(transcript.getProperties().getOrDefault("gene_name", "."));
                pw.print("\t");
                pw.print(transcript.getProperties().getOrDefault("transcript_type", "."));
                pw.print("\t");
                pw.print(gene.getStrand());
                pw.print("\t");
                pw.print(transcript.getId());
                pw.print("\t");
                pw.print(gene.getId());
                pw.print("\t");
                pw.print(part.intervals.stream().map(R -> String.valueOf(R.getStart()) + "-" + R.getEnd()).collect(Collectors.joining(";")));
                pw.print("\t");
                pw.print(fisher.p_value);
                pw.print("\t");
                pw.print(fisher.affected_alt);
                pw.print("\t");
                pw.print(fisher.affected_hom);
                pw.print("\t");
                pw.print(fisher.unaffected_alt);
                pw.print("\t");
                pw.print(fisher.unaffected_hom);
                pw.print("\t");
                pw.print(variants.size());
                pw.println();
            }
        }
    }
    progress.close();
    final ProgressFactory.Watcher<SimpleInterval> progress2 = ProgressFactory.newInstance().logger(LOG).dictionary(vcfDict).build();
    /**
     * scan intergenics ...
     */
    for (final SimpleInterval intergenic : all_intergenic) {
        progress2.apply(intergenic);
        final int intergenic_window_size = 2000;
        final int intergenic_window_shifr = 100;
        final List<SimpleInterval> parts = new ArrayList<>();
        if (intergenic.getLengthOnReference() <= intergenic_window_size)
            continue;
        int start_pos = intergenic.getStart();
        while (start_pos + intergenic_window_size <= intergenic.getEnd()) {
            int xend = Math.min(intergenic.getEnd(), start_pos + intergenic_window_size - 1);
            int xstart = xend - intergenic_window_size - 1;
            parts.add(new SimpleInterval(intergenic.getContig(), xstart, xend));
            start_pos += intergenic_window_shifr;
        }
        for (final SimpleInterval part : parts) {
            final List<VariantContext> variants = vcfReader.query(part).stream().filter(V -> accept(V)).collect(Collectors.toList());
            if (variants.isEmpty())
                continue;
            final FisherResult fisher = runFisher(variants);
            if (fisher.p_value > this.fisherTreshold)
                continue;
            final String label = "intergenic_" + part.getStart() + "_" + part.getEnd();
            if (vcw != null) {
                for (final VariantContext ctx : variants) {
                    vcw.add(new VariantContextBuilder(ctx).attribute(BURDEN_KEY, VCFUtils.escapeInfoField(label)).make());
                }
            }
            pw.print(part.getContig());
            pw.print("\t");
            pw.print(part.getStart() - 1);
            pw.print("\t");
            pw.print(part.getEnd());
            pw.print("\t");
            pw.print(label);
            pw.print("\t");
            pw.print(part.getLengthOnReference());
            pw.print("\t");
            pw.print(".");
            pw.print("\t");
            pw.print("intergenic");
            pw.print("\t");
            pw.print(".");
            pw.print("\t");
            pw.print(".");
            pw.print("\t");
            pw.print(".");
            pw.print("\t");
            pw.print("" + part.getStart() + "-" + part.getEnd());
            pw.print("\t");
            pw.print(fisher.p_value);
            pw.print("\t");
            pw.print(fisher.affected_alt);
            pw.print("\t");
            pw.print(fisher.affected_hom);
            pw.print("\t");
            pw.print(fisher.unaffected_alt);
            pw.print("\t");
            pw.print(fisher.unaffected_hom);
            pw.print("\t");
            pw.print(variants.size());
            pw.println();
        }
    }
    progress2.close();
}

Example 7 with Gene

use of com.github.lindenb.jvarkit.util.bio.structure.Gene in project jvarkit by lindenb.

the class VcfGtfSplitter method doWork.

@Override
public int doWork(final List<String> args) {
    ArchiveFactory archiveFactory = null;
    PrintWriter manifest = null;
    VCFReader vcfFileReader = null;
    try {
        this.attCleaner = AttributeCleaner.compile(this.xannotatePattern);
        for (final String s : featuresString.split("[;, ]")) {
            if (StringUtils.isBlank(s))
                continue;
            if (s.equals("cds")) {
                use_cds = true;
            } else if (s.equals("intron")) {
                use_cds = true;
            } else if (s.equals("exon")) {
                use_exon = true;
            } else if (s.equals("stop")) {
                use_stop = true;
            } else if (s.equals("start")) {
                use_start = true;
            } else if (s.equals("transcript")) {
                use_exon = true;
                use_intron = true;
            } else if (s.equals("utr5")) {
                use_utr5 = true;
            } else if (s.equals("utr3")) {
                use_utr3 = true;
            } else if (s.equals("utr")) {
                use_utr3 = true;
                use_utr5 = true;
            } else if (s.equals("upstream")) {
                use_upstream = true;
            } else if (s.equals("downstream")) {
                use_downstream = true;
            } else if (s.equals("splice")) {
                use_splice = true;
            } else if (s.equals("cds_utr5")) {
                use_cds_utr5 = true;
            } else if (s.equals("cds_utr3")) {
                use_cds_utr3 = true;
            } else if (s.equals("cds_utr")) {
                use_cds_utr3 = true;
                use_cds_utr5 = true;
            } else {
                LOG.error("unknown code " + s + " in " + this.featuresString);
                return -1;
            }
        }
        final Path tmpVcf = Files.createTempFile("tmp.", (use_bcf ? FileExtensions.BCF : FileExtensions.COMPRESSED_VCF));
        String input = oneAndOnlyOneFile(args);
        vcfFileReader = VCFReaderFactory.makeDefault().open(Paths.get(input), true);
        final VCFHeader header1 = vcfFileReader.getHeader();
        final SAMSequenceDictionary dict = header1.getSequenceDictionary();
        if (dict == null && this.use_bcf) {
            throw new JvarkitException.VcfDictionaryMissing(input);
        }
        if (dict != null && !limitToContigs.isEmpty()) {
            final ContigNameConverter ctgNameConverter = ContigNameConverter.fromOneDictionary(dict);
            final Set<String> set2 = new HashSet<>(this.limitToContigs.size());
            for (final String ctg : this.limitToContigs) {
                final String ctg2 = ctgNameConverter.apply(ctg);
                if (StringUtils.isBlank(ctg2)) {
                    LOG.error(JvarkitException.ContigNotFoundInDictionary.getMessage(ctg, dict));
                    return -1;
                }
                set2.add(ctg2);
            }
            this.limitToContigs = set2;
        }
        final List<Gene> all_genes;
        try (GtfReader gtfReader = new GtfReader(this.gtfPath)) {
            final Comparator<Gene> cmp;
            if (dict != null) {
                gtfReader.setContigNameConverter(ContigNameConverter.fromOneDictionary(dict));
                cmp = new ContigDictComparator(dict).createLocatableComparator();
            } else {
                cmp = (A, B) -> {
                    final int i = A.getContig().compareTo(B.getContig());
                    if (i != 0)
                        return i;
                    return Integer.compare(A.getStart(), B.getStart());
                };
            }
            all_genes = gtfReader.getAllGenes().stream().filter(G -> {
                if (this.protein_coding_only && !"protein_coding".equals(G.getGeneBiotype()))
                    return false;
                if (this.limitToContigs.isEmpty())
                    return true;
                return this.limitToContigs.contains(G.getContig());
            }).sorted(cmp).collect(Collectors.toList());
        }
        archiveFactory = ArchiveFactory.open(this.outputFile);
        archiveFactory.setCompressionLevel(0);
        manifest = new PrintWriter(this.manifestFile == null ? new NullOuputStream() : IOUtils.openPathForWriting(manifestFile));
        manifest.println("#chrom\tstart\tend\tGene-Id\tGene-Name\tGene-Biotype\tTranscript-Id\tpath\tCount_Variants");
        if (this.split_by_transcript) {
            final Iterator<Transcript> triter = all_genes.stream().flatMap(G -> G.getTranscripts().stream()).iterator();
            while (triter.hasNext()) {
                final Transcript tr = triter.next();
                final AbstractSplitter splitter = new TranscriptSplitter(tr);
                this.split(splitter, vcfFileReader, header1, dict, archiveFactory, tmpVcf, manifest);
            }
        } else {
            for (Gene gene : all_genes) {
                final AbstractSplitter splitter = new GeneSplitter(gene);
                this.split(splitter, vcfFileReader, header1, dict, archiveFactory, tmpVcf, manifest);
            }
        }
        vcfFileReader.close();
        vcfFileReader = null;
        manifest.flush();
        manifest.close();
        manifest = null;
        archiveFactory.close();
        Files.deleteIfExists(tmpVcf);
        return RETURN_OK;
    } catch (final Exception err) {
        LOG.error(err);
        return -1;
    } finally {
        CloserUtil.close(vcfFileReader);
        CloserUtil.close(archiveFactory);
        CloserUtil.close(manifest);
    }
}

Example 8 with Gene

use of com.github.lindenb.jvarkit.util.bio.structure.Gene in project jvarkit by lindenb.

the class PlotSashimi method plotSashimi.

/**
 * create the SVG itself
 */
private void plotSashimi(final ArchiveFactory archive, final SamReader samReader, final Locatable interval, final Path bamPath, final PrintWriter manifest) {
    final int drawing_width = Math.max(100, this.image_width_pixel);
    final int coverageHeight = Math.max(100, Integer.parseInt(this.dynamicParams.getOrDefault("coverage.height", "300")));
    final double pixelperbase = drawing_width / (double) interval.getLengthOnReference();
    final SAMFileHeader header = samReader.getFileHeader();
    final Collection<Gene> genes = this.geneMap.getOverlapping(interval);
    final Set<String> geneNames = genes.stream().map(G -> G.getGeneName()).filter(S -> !StringUtils.isBlank(S)).collect(Collectors.toCollection(TreeSet::new));
    /**
     * extract the sample name or just use the filename
     */
    final String sampleName = StringUtils.ifBlank(header.getReadGroups().stream().map(G -> this.partition.apply(G)).filter(S -> !StringUtils.isBlank(S)).sorted().collect(Collectors.joining(";")), bamPath.getFileName().toString());
    final Function<Integer, Double> pos2pixel = POS -> (POS - interval.getStart()) / (double) interval.getLengthOnReference() * drawing_width;
    final Counter<SimpleInterval> gaps = new Counter<>();
    final int[] coverage = new int[interval.getLengthOnReference()];
    try (SAMRecordIterator iter = samReader.queryOverlapping(interval.getContig(), interval.getStart(), interval.getEnd())) {
        /**
         * no read here, skip
         */
        boolean got_one = false;
        while (iter.hasNext()) {
            final SAMRecord rec = iter.next();
            if (rec.getReadUnmappedFlag())
                continue;
            if (rec.getReadFailsVendorQualityCheckFlag())
                continue;
            if (rec.isSecondaryOrSupplementary())
                continue;
            if (rec.getDuplicateReadFlag())
                continue;
            if (rec.getMappingQuality() < this.min_mapq)
                continue;
            final Cigar cigar = rec.getCigar();
            if (cigar == null || cigar.isEmpty())
                continue;
            got_one = true;
            int ref = rec.getAlignmentStart();
            for (final CigarElement ce : cigar) {
                if (ref > interval.getEnd())
                    break;
                final CigarOperator op = ce.getOperator();
                if (op.equals(CigarOperator.N) || (use_D_operator && op.equals(CigarOperator.D))) {
                    gaps.incr(new SimpleInterval(rec.getContig(), ref, ref + ce.getLength() - 1));
                }
                if (op.consumesReferenceBases()) {
                    if (op.consumesReadBases()) {
                        for (int x = 0; x < ce.getLength(); ++x) {
                            final int pos1 = ref + x;
                            if (pos1 < interval.getStart())
                                continue;
                            if (pos1 > interval.getEnd())
                                break;
                            coverage[pos1 - interval.getStart()]++;
                        }
                    }
                    ref += ce.getLength();
                }
            }
        }
        if (!got_one && this.skip_region_without_read)
            return;
    }
    final int max_coverage;
    if (this.force_max_coverage > 0) {
        max_coverage = this.force_max_coverage;
    } else {
        max_coverage = Math.max(1, Arrays.stream(coverage).max().orElse(0));
    }
    while (this.document.hasChildNodes()) {
        this.document.removeChild(this.document.getFirstChild());
    }
    final Element svgRoot = element("svg");
    this.document.appendChild(svgRoot);
    /* SVG title */
    {
        final Element title = element("title");
        svgRoot.appendChild(title);
        title.appendChild(text(interval.toString() + (!geneNames.isEmpty() && geneNames.size() < 3 ? " " + String.join(" ", geneNames) : "")));
    }
    /* SVG style */
    {
        final Element style = element("style");
        svgRoot.appendChild(style);
        style.appendChild(text(this.cssPath == null ? ".coverage { fill:red;fill:url('#grad01')} " + ".maintitle {text-anchor:middle;fill:blue} " + ".sample {fill:blue;font-size:7px;} " + ".frame { fill:none; stroke: darkgray;} " + ".arcK { fill:none; stroke: blue; stroke-linecap:round;opacity:0.8;} " + ".arcU { fill:none; stroke: red; stroke-linecap:round;opacity:0.8;} " + ".transcript { fill:darkgray; stroke: darkgray;} " + ".exon { fill:green; stroke: darkgray;} " + ".frame { fill:none; stroke: darkgray;} " + ".rulerline {stroke:lightgray;stroke-width:0.5px;}\n" + ".exonline {stroke:green;stroke-width:0.5px;opacity:0.5;}\n" + ".rulerlabel {stroke:gray;stroke-width:0.5px;font-size:7px;}\n" + "a {cursor: pointer;}\n" : IOUtils.slurpPath(this.cssPath)));
    }
    // SVG def
    {
        final Element defs = element("defs");
        svgRoot.appendChild(defs);
        // linear gradient
        {
            Element grad = element("linearGradient");
            defs.appendChild(grad);
            grad.setAttribute("id", "grad01");
            grad.setAttribute("gradientTransform", "rotate(90)");
            Element stop = element("stop");
            grad.appendChild(stop);
            stop.setAttribute("offset", "0%");
            stop.setAttribute("stop-color", (max_coverage > 50 ? "red" : max_coverage > 20 ? "green" : "blue"));
            stop = element("stop");
            grad.appendChild(stop);
            stop.setAttribute("offset", "100%");
            stop.setAttribute("stop-color", "darkblue");
        }
    }
    final Element descr = element("desc");
    svgRoot.appendChild(descr);
    descr.appendChild(text("Author: Pierre Lindenbaum\n" + JVarkitVersion.getInstance().getCompilationDate() + "\n" + JVarkitVersion.getInstance().getGitHash()));
    final Element maing = element("g");
    svgRoot.appendChild(maing);
    int y = 0;
    // main title
    Element gtitle = element("text", new SimpleInterval(interval).toNiceString() + (StringUtils.isBlank(sampleName) ? "" : " " + sampleName) + (geneNames.isEmpty() ? "" : " " + String.join(" ", geneNames)));
    gtitle.setAttribute("class", "maintitle");
    gtitle.setAttribute("x", format(drawing_width / 2));
    gtitle.setAttribute("y", "15");
    svgRoot.appendChild(gtitle);
    y += 20;
    // sample name
    if (!StringUtils.isBlank(sampleName)) {
        gtitle = element("text", sampleName);
        gtitle.setAttribute("class", "sample");
        gtitle.setAttribute("x", "5");
        gtitle.setAttribute("y", "20");
        svgRoot.appendChild(gtitle);
    }
    y += 50;
    final int prev_y = y;
    /**
     * horizontal ruler
     */
    {
        final Element ruler_gh = element("g");
        maing.appendChild(ruler_gh);
        final int sep = bestTicks(interval.getLengthOnReference());
        for (int pos = interval.getStart(); pos <= interval.getEnd(); ++pos) {
            if (pos % sep != 0)
                continue;
            double x = pos2pixel.apply(pos);
            final Element line = element("line");
            ruler_gh.appendChild(line);
            line.setAttribute("class", "rulerline");
            line.appendChild(element("title", StringUtils.niceInt(pos)));
            line.setAttribute("x1", format(x));
            line.setAttribute("x2", format(x));
            line.setAttribute("y1", format(y));
            line.setAttribute("y2", format(y + coverageHeight));
            final Element label = element("text", StringUtils.niceInt(pos));
            label.setAttribute("class", "rulerlabel");
            label.setAttribute("x", "0");
            label.setAttribute("y", "0");
            label.setAttribute("transform", "translate(" + format(x) + "," + y + ") rotate(90) ");
            ruler_gh.appendChild(label);
        }
    }
    /**
     * vertical ruler
     */
    {
        final Element ruler_gv = element("g");
        maing.appendChild(ruler_gv);
        final int sep = bestTicks(max_coverage);
        for (int pos = 0; pos <= max_coverage; ++pos) {
            if (pos % sep != 0)
                continue;
            double ry = (int) (y + coverageHeight - (pos / (double) max_coverage) * coverageHeight);
            final Element line = element("line");
            ruler_gv.appendChild(line);
            line.setAttribute("class", "rulerline");
            line.appendChild(element("title", StringUtils.niceInt(pos)));
            line.setAttribute("x1", format(0));
            line.setAttribute("x2", format(drawing_width));
            line.setAttribute("y1", format(ry));
            line.setAttribute("y2", format(ry));
            final Element label = element("text", StringUtils.niceInt(pos));
            label.setAttribute("class", "rulerlabel");
            label.setAttribute("x", "1");
            label.setAttribute("y", format(ry));
            ruler_gv.appendChild(label);
        }
    }
    /**
     * vertical lines of exons
     */
    final Element exon_v = element("g");
    final Element covPath = element("path");
    covPath.setAttribute("class", "coverage");
    maing.appendChild(covPath);
    final StringBuilder sb = new StringBuilder();
    sb.append("M 0 " + format(y + coverageHeight));
    for (int k = 0; k < coverage.length; k++) {
        // if(k+1< coverage.length && coverage[k]==coverage[k+1]) continue;
        final double dpy = y + coverageHeight - coverageHeight * (coverage[k] / (double) max_coverage);
        sb.append(" L " + format(pixelperbase * k) + " " + format(dpy));
    }
    sb.append(" L " + format(drawing_width) + " " + format(y + coverageHeight));
    sb.append(" Z");
    covPath.setAttribute("d", sb.toString());
    covPath.appendChild(element("title", "Coverage. Max:" + StringUtils.niceInt(max_coverage)));
    int next_y = y + coverageHeight;
    /* plot arc */
    if (!gaps.isEmpty()) {
        boolean drawAbove = true;
        int max_occurence = (int) gaps.count(gaps.getMostFrequent());
        for (final SimpleInterval intron : gaps.keySet()) {
            final int occurence = (int) gaps.count(intron);
            boolean is_known_intron = genes.stream().flatMap(G -> G.getTranscripts().stream()).flatMap(T -> T.getIntrons().stream()).filter(E -> E.overlaps(intron)).anyMatch(I -> I.getStart() == intron.getStart() && I.getEnd() == intron.getEnd());
            final int junctionStart = intron.getStart() - 1;
            final int junctionEnd = intron.getEnd() + 1;
            if (!CoordMath.encloses(interval.getStart(), interval.getEnd(), junctionStart, junctionEnd))
                continue;
            final double xstart = pos2pixel.apply(junctionStart);
            final double xend = pos2pixel.apply(junctionEnd);
            double ystart = y + coverageHeight - coverageHeight * (coverage[junctionStart - interval.getStart()] / (double) max_coverage);
            double yend = y + coverageHeight - coverageHeight * (coverage[junctionEnd - interval.getStart()] / (double) max_coverage);
            final Element arc = element("path");
            sb.setLength(0);
            double x_mid = (xend - xstart) / 2.0;
            double x2 = xstart + x_mid;
            final double y2;
            // small gap: always print it under xaxis
            if (xend - xstart < 30)
                drawAbove = true;
            if (drawAbove) {
                ystart = y + coverageHeight;
                yend = y + coverageHeight;
                y2 = y + coverageHeight + x_mid;
                next_y = (int) Math.max(next_y, y + coverageHeight + x_mid / 2 + 10);
            } else {
                y2 = Math.max(0, ystart + (yend - ystart) / 2.0 - x_mid);
            }
            sb.append("M " + format(xstart) + " " + format(ystart));
            sb.append(" Q " + format(x2) + " " + format(y2) + " " + format(xend) + " " + format(yend));
            arc.setAttribute("d", sb.toString());
            arc.setAttribute("class", "arc" + (is_known_intron ? "K" : "U"));
            final double stroke_width = 1 + /* show very small one */
            (occurence / (double) max_occurence) * 10;
            arc.setAttribute("style", "stroke-width:" + format(stroke_width) + "px;");
            arc.appendChild(element("title", new SimpleInterval(interval.getContig(), junctionStart, junctionEnd).toNiceString() + " (" + StringUtils.niceInt(occurence) + ") " + (is_known_intron ? "known" : "unknown")));
            maing.appendChild(wrapLoc(arc, intron));
            drawAbove = !drawAbove;
        }
    }
    y = next_y;
    y += 2;
    /**
     * pileup transcripts
     */
    final List<List<Transcript>> transcriptRows = new ArrayList<>();
    for (final Transcript transcript : genes.stream().flatMap(L -> L.getTranscripts().stream()).filter(T -> T.overlaps(interval)).sorted((A, B) -> Integer.compare(A.getStart(), B.getStart())).collect(Collectors.toList())) {
        int rowidx = 0;
        while (rowidx < transcriptRows.size()) {
            final List<Transcript> row = transcriptRows.get(rowidx);
            final Transcript last = row.get(row.size() - 1);
            if (!last.overlaps(transcript)) {
                row.add(transcript);
                break;
            }
            rowidx++;
        }
        if (rowidx == transcriptRows.size()) {
            final List<Transcript> row = new ArrayList<>();
            row.add(transcript);
            transcriptRows.add(row);
        }
    }
    /**
     * plot transcripts
     */
    final Element transcripts_g = element("g");
    maing.appendChild(transcripts_g);
    final int transcript_height = Math.max(10, Integer.parseInt(this.dynamicParams.getOrDefault("transcript.height", "12")));
    for (final List<Transcript> row : transcriptRows) {
        final Element grow = element("g");
        transcripts_g.appendChild(grow);
        for (final Transcript transcript : row) {
            final Element transcript_g = element("g");
            grow.appendChild(transcript_g);
            final Element tr = element("line");
            final double midy = y + transcript_height / 2.0;
            tr.setAttribute("class", "transcript");
            double tr_x1 = Math.max(1.0, pos2pixel.apply(transcript.getStart()));
            tr.setAttribute("x1", format(tr_x1));
            tr.setAttribute("y1", format(midy));
            tr.setAttribute("x2", format(Math.min(drawing_width, pos2pixel.apply(transcript.getEnd()))));
            tr.setAttribute("y2", format(midy));
            tr.appendChild(element("title", transcript.getId() + " " + transcript.getGene().getGeneName()));
            transcript_g.appendChild(wrapLoc(tr, transcript));
            final Element label = element("text", transcript.getId() + " " + transcript.getGene().getGeneName());
            label.setAttribute("class", "rulerlabel");
            label.setAttribute("x", format(tr_x1));
            label.setAttribute("y", format(midy));
            transcript_g.appendChild(label);
            for (final Exon exon : transcript.getExons()) {
                if (!exon.overlaps(interval))
                    continue;
                final Element exon_rect = element("rect");
                exon_rect.setAttribute("class", "exon");
                final double exonx1 = Math.max(1.0, pos2pixel.apply(exon.getStart()));
                final double exonx2 = Math.min(drawing_width, pos2pixel.apply(exon.getEnd()));
                exon_rect.setAttribute("x", format(exonx1));
                exon_rect.setAttribute("y", format(y));
                exon_rect.setAttribute("height", format(transcript_height));
                exon_rect.setAttribute("width", format(exonx2 - exonx1));
                exon_rect.appendChild(element("title", exon.getName() + " " + transcript.getId() + " " + transcript.getGene().getGeneName()));
                transcript_g.appendChild(wrapLoc(exon_rect, exon));
                for (int side = 0; side < 2; ++side) {
                    final double x = pos2pixel.apply(side == 0 ? exon.getStart() : exon.getEnd());
                    final Element line = element("line");
                    exon_v.appendChild(line);
                    line.setAttribute("class", "exonline");
                    line.setAttribute("x1", format(x));
                    line.setAttribute("x2", format(x));
                    line.setAttribute("y2", format(y + transcript_height));
                    line.setAttribute("y1", format(prev_y));
                }
            }
        }
        y += transcript_height + 2;
    }
    maing.appendChild(exon_v);
    /* final frame */
    final Element frame_rect = element("rect");
    frame_rect.setAttribute("class", "frame");
    frame_rect.setAttribute("x", "0");
    frame_rect.setAttribute("y", "0");
    frame_rect.setAttribute("width", format(drawing_width));
    frame_rect.setAttribute("height", format(y));
    svgRoot.appendChild(frame_rect);
    svgRoot.setAttribute("width", format(drawing_width + 1));
    svgRoot.setAttribute("height", format(y + 1));
    try {
        final Transformer tr = TransformerFactory.newInstance().newTransformer();
        final String md5 = StringUtils.md5(interval.getContig() + ":" + interval.getStart() + ":" + interval.getEnd() + ":" + bamPath.toString());
        final String filename = md5.substring(0, 2) + File.separatorChar + md5.substring(2) + File.separator + interval.getContig() + "_" + interval.getStart() + "_" + interval.getEnd() + (StringUtils.isBlank(sampleName) ? "" : "." + sampleName.replaceAll("[/\\:]", "_")) + ".svg" + (this.compressed_svg ? ".gz" : "");
        if (this.compressed_svg) {
            try (final OutputStream pw = archive.openOuputStream(filename)) {
                try (GZIPOutputStream gzout = new GZIPOutputStream(pw)) {
                    tr.transform(new DOMSource(this.document), new StreamResult(gzout));
                    gzout.finish();
                    gzout.flush();
                }
                pw.flush();
            }
        } else {
            try (final PrintWriter pw = archive.openWriter(filename)) {
                tr.transform(new DOMSource(this.document), new StreamResult(pw));
                pw.flush();
            }
        }
        manifest.print(interval.getContig());
        manifest.print('\t');
        manifest.print(interval.getStart() - 1);
        manifest.print('\t');
        manifest.print(interval.getEnd());
        manifest.print('\t');
        manifest.print(bamPath.toString());
        manifest.print('\t');
        manifest.print(geneNames.isEmpty() ? "." : String.join(",", geneNames));
        manifest.print('\t');
        manifest.print(StringUtils.isBlank(sampleName) ? "." : sampleName);
        manifest.print('\t');
        manifest.print((archive.isTarOrZipArchive() ? "" : this.outputFile.toString() + File.separator) + filename);
        manifest.println();
    } catch (final Exception err) {
        throw new RuntimeException(err);
    }
}

Example 9 with Gene

use of com.github.lindenb.jvarkit.util.bio.structure.Gene in project jvarkit by lindenb.

the class GtfRetroCopy method doWork.

@Override
public int doWork(final List<String> args) {
    VCFReader vcfFileReader = null;
    VariantContextWriter vcw0 = null;
    try {
        /* load the reference genome */
        /* create a contig name converter from the REF */
        final Set<String> knownGeneIds;
        if (this.knownPath != null) {
            try (BufferedReader br = IOUtils.openPathForBufferedReading(this.knownPath)) {
                knownGeneIds = br.lines().filter(L -> !StringUtils.isBlank(L)).map(S -> S.trim()).filter(S -> !(S.equals("-") || S.equals(".") || S.startsWith("#"))).collect(Collectors.toSet());
            }
        } else {
            knownGeneIds = Collections.emptySet();
        }
        // open the sam file
        final String input = oneAndOnlyOneFile(args);
        vcfFileReader = VCFReaderFactory.makeDefault().open(Paths.get(input), true);
        final VCFHeader header = vcfFileReader.getHeader();
        final SAMSequenceDictionary dict = header.getSequenceDictionary();
        final Comparator<String> contigCmp = dict == null ? (A, B) -> A.compareTo(B) : new ContigDictComparator(dict);
        final Comparator<Gene> geneCmp = (A, B) -> {
            int i = contigCmp.compare(A.getContig(), B.getContig());
            if (i != 0)
                return i;
            i = Integer.compare(A.getStart(), B.getStart());
            if (i != 0)
                return i;
            return Integer.compare(A.getEnd(), B.getEnd());
        };
        final GtfReader gtfReader = new GtfReader(this.gtfPath);
        if (dict != null && !dict.isEmpty()) {
            this.writingVcf.dictionary(dict);
            gtfReader.setContigNameConverter(ContigNameConverter.fromOneDictionary(dict));
        }
        final List<Gene> genes = gtfReader.getAllGenes().stream().filter(G -> G.getTranscripts().stream().count() > 0L).filter(G -> G.getTranscripts().stream().anyMatch(T -> T.getIntronCount() >= this.min_intron_count)).sorted(geneCmp).collect(Collectors.toList());
        gtfReader.close();
        /**
         * build vcf header
         */
        final Set<VCFHeaderLine> metaData = new HashSet<>();
        metaData.add(VCFStandardHeaderLines.getFormatLine(VCFConstants.GENOTYPE_KEY, true));
        metaData.add(VCFStandardHeaderLines.getFormatLine(VCFConstants.GENOTYPE_QUALITY_KEY, true));
        metaData.add(VCFStandardHeaderLines.getFormatLine(VCFConstants.DEPTH_KEY, true));
        metaData.add(VCFStandardHeaderLines.getFormatLine(VCFConstants.GENOTYPE_ALLELE_DEPTHS, true));
        metaData.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.DEPTH_KEY, true));
        metaData.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_NUMBER_KEY, true));
        metaData.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_COUNT_KEY, true));
        metaData.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_COUNT_KEY, true));
        metaData.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_FREQUENCY_KEY, true));
        metaData.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.END_KEY, true));
        metaData.add(new VCFInfoHeaderLine(VCFConstants.SVTYPE, 1, VCFHeaderLineType.String, "Variation type"));
        metaData.add(new VCFInfoHeaderLine("SVLEN", 1, VCFHeaderLineType.Integer, "Variation Length"));
        metaData.add(new VCFInfoHeaderLine(ATT_INTRONS_BOUNDS, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String, "Introns boundaries"));
        metaData.add(new VCFInfoHeaderLine(ATT_INTRONS_SIZES, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Integer, "Introns sizes"));
        metaData.add(new VCFFilterHeaderLine(ATT_NOT_ALL_INTRONS, "Not all introns were found retrocopied"));
        for (final String att : ENSEMBL_TRANSCRIPT_ATTS) {
            metaData.add(new VCFInfoHeaderLine(att, 1, VCFHeaderLineType.String, "Value for the attribute '" + att + "' in the gtf"));
        }
        // metaData.add(new VCFFormatHeaderLine(ATT_COUNT_SUPPORTING_READS, 2,VCFHeaderLineType.Integer,"Count supporting reads [intron-left/intron-right]"));
        // metaData.add(new VCFInfoHeaderLine(ATT_RETRO_DESC, VCFHeaderLineCount.UNBOUNDED,VCFHeaderLineType.String,
        // "Retrocopy attributes: transcript-id|strand|exon-left|exon-left-bases|exon-right-bases|exon-right"));
        metaData.add(new VCFInfoHeaderLine(ATT_INTRONS_COUNT, 1, VCFHeaderLineType.Integer, "Number of introns for the Transcript"));
        metaData.add(new VCFInfoHeaderLine(ATT_INTRONS_CANDIDATE_COUNT, 1, VCFHeaderLineType.Integer, "Number of introns found retrocopied for the transcript"));
        metaData.add(new VCFInfoHeaderLine(ATT_INTRONS_CANDIDATE_FRACTION, 1, VCFHeaderLineType.Float, "Fraction of introns found retrocopied for the transcript"));
        metaData.add(new VCFFilterHeaderLine(ATT_NOT_ALL_INTRONS, "Not all introns were found retrocopied"));
        metaData.add(new VCFFilterHeaderLine(ATT_KNOWN, "Known RetroGenes. " + (this.knownPath == null ? "" : " Source: " + this.knownPath)));
        final VCFHeader header2 = new VCFHeader(header);
        metaData.stream().forEach(H -> header2.addMetaDataLine(H));
        JVarkitVersion.getInstance().addMetaData(this, header2);
        final Allele ref = Allele.create((byte) 'N', true);
        final Allele alt = Allele.create("<RETROCOPY>", false);
        /* open vcf for writing*/
        vcw0 = this.writingVcf.open(this.outputFile);
        vcw0.writeHeader(header2);
        final ProgressFactory.Watcher<Gene> progress = ProgressFactory.newInstance().logger(LOG).dictionary(dict).build();
        for (final Gene gene : genes) {
            progress.apply(gene);
            final List<VariantContext> variants = new ArrayList<>();
            final CloseableIterator<VariantContext> iter2 = vcfFileReader.query(gene.getContig(), gene.getStart(), gene.getEnd());
            while (iter2.hasNext()) {
                final VariantContext ctx = iter2.next();
                // SNV
                if (ctx.getStart() == ctx.getEnd())
                    continue;
                StructuralVariantType svType = ctx.getStructuralVariantType();
                if (StructuralVariantType.BND.equals(svType))
                    continue;
                if (StructuralVariantType.INS.equals(svType))
                    continue;
                variants.add(ctx);
            }
            iter2.close();
            if (variants.isEmpty())
                continue;
            for (final Transcript transcript : gene.getTranscripts()) {
                if (!transcript.hasIntron())
                    continue;
                if (transcript.getIntronCount() < this.min_intron_count)
                    continue;
                final Counter<String> samples = new Counter<>();
                for (final Intron intron : transcript.getIntrons()) {
                    for (final VariantContext ctx : variants) {
                        if (!isWithinDistance(intron.getStart(), ctx.getStart()))
                            continue;
                        if (!isWithinDistance(intron.getEnd(), ctx.getEnd()))
                            continue;
                        if (ctx.hasGenotypes()) {
                            for (final Genotype g : ctx.getGenotypes()) {
                                if (g.isNoCall() || g.isHomRef())
                                    continue;
                                samples.incr(g.getSampleName());
                            }
                        } else {
                            samples.incr("*");
                        }
                    }
                // end iter2
                }
                // end intron
                final long max_count = samples.stream().mapToLong(E -> E.getValue()).max().orElse(0L);
                if (max_count == 0)
                    continue;
                if (this.only_all_introns && max_count != transcript.getIntronCount())
                    continue;
                // ok good candidate
                final VariantContextBuilder vcb = new VariantContextBuilder();
                vcb.chr(transcript.getContig());
                vcb.start(transcript.getStart());
                vcb.stop(transcript.getEnd());
                switch(this.idKey) {
                    case gene_name:
                        final String gn = transcript.getGene().getGeneName();
                        vcb.id(StringUtils.isBlank(gn) ? transcript.getId() : gn);
                        break;
                    case gene_id:
                        vcb.id(transcript.getGene().getId());
                        break;
                    case transcript_id:
                        vcb.id(transcript.getId());
                        break;
                    default:
                        throw new IllegalStateException();
                }
                final List<Allele> alleles = Arrays.asList(ref, alt);
                // vcb.attribute(VCFConstants.ALLELE_NUMBER_KEY,2);
                // vcb.attribute(VCFConstants.ALLELE_COUNT_KEY,1);
                // vcb.attribute(VCFConstants.ALLELE_FREQUENCY_KEY,0.5);
                vcb.attribute(VCFConstants.SVTYPE, "DEL");
                vcb.attribute(VCFConstants.END_KEY, transcript.getEnd());
                vcb.attribute("SVLEN", transcript.getLengthOnReference());
                vcb.attribute(ATT_INTRONS_BOUNDS, transcript.getIntrons().stream().map(S -> "" + S.getStart() + "-" + S.getEnd()).collect(Collectors.toList()));
                vcb.attribute(ATT_INTRONS_SIZES, transcript.getIntrons().stream().mapToInt(S -> S.getLengthOnReference()).toArray());
                for (final String att : ENSEMBL_TRANSCRIPT_ATTS) {
                    final String v = transcript.getProperties().get(att);
                    if (StringUtils.isBlank(v))
                        continue;
                    vcb.attribute(att, v);
                }
                vcb.alleles(alleles);
                boolean pass_filter = true;
                // introns sequences
                vcb.attribute(ATT_INTRONS_CANDIDATE_COUNT, max_count);
                vcb.attribute(ATT_INTRONS_COUNT, transcript.getIntronCount());
                vcb.attribute(ATT_INTRONS_CANDIDATE_FRACTION, max_count / (float) transcript.getIntronCount());
                if (transcript.getIntronCount() != max_count) {
                    vcb.filter(ATT_NOT_ALL_INTRONS);
                    pass_filter = false;
                }
                if (knownGeneIds.contains(transcript.getGene().getId())) {
                    vcb.filter(ATT_KNOWN);
                    pass_filter = false;
                }
                if (header.hasGenotypingData()) {
                    final List<Genotype> genotypes = new ArrayList<>();
                    for (final String sn : header.getSampleNamesInOrder()) {
                        final List<Allele> gtalleles;
                        if (samples.count(sn) == 0L) {
                            gtalleles = Arrays.asList(ref, ref);
                        } else {
                            gtalleles = Arrays.asList(ref, alt);
                        }
                        final GenotypeBuilder gb = new GenotypeBuilder(sn, gtalleles);
                        genotypes.add(gb.make());
                    }
                    vcb.genotypes(genotypes);
                }
                if (pass_filter)
                    vcb.passFilters();
                vcw0.add(vcb.make());
            }
        }
        progress.close();
        vcw0.close();
        vcfFileReader.close();
        vcfFileReader = null;
        return 0;
    } catch (final Exception err) {
        LOG.error(err);
        return -1;
    } finally {
        CloserUtil.close(vcfFileReader);
        CloserUtil.close(vcw0);
    }
}