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

Example 16 with Transcript

use of com.github.lindenb.jvarkit.util.bio.structure.Transcript 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 17 with Transcript

use of com.github.lindenb.jvarkit.util.bio.structure.Transcript 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);
    }
}

Example 18 with Transcript

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

the class VcfToPostscript method run.

private void run(final VCFIterator in) {
    for (; ; ) {
        VariantContext ctx = null;
        if (in.hasNext())
            ctx = in.next();
        if (ctx == null || this.genes.isEmpty() || (!this.genes.isEmpty() && !this.genes.get(0).getContig().equals(ctx.getContig())) || (!this.genes.isEmpty() && this.chromEnd <= ctx.getStart())) {
            this.print();
            if (this.outw.checkError())
                return;
            if (ctx == null)
                return;
            this.clear();
            for (Transcript g : chrom2transcript.getOrDefault(ctx.getContig(), Collections.emptyList())) {
                if (this.genes.isEmpty()) {
                    if (g.getTxEnd() <= ctx.getStart() || g.getTxStart() > ctx.getEnd()) {
                        continue;
                    }
                    this.addGene(g);
                } else {
                    if (!(g.getTxStart() > this.chromEnd || g.getTxEnd() <= this.chromStart)) {
                        this.addGene(g);
                    }
                }
            }
        }
        if (!genes.isEmpty() && ctx.getStart() - 1 >= this.chromStart && ctx.getStart() <= this.chromEnd) {
            this.addVariant(ctx);
        }
    }
}

Example 19 with Transcript

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

the class VcfToPostscript method print.

private void print() {
    if (this.positions.isEmpty()) {
        return;
    }
    ++count_pages_printed;
    final Transcript first = genes.get(0);
    final double fHeight = 20;
    final Dimension localPage = new Dimension((int) (this.pageDef.width), (int) (margin.top + margin.bottom + (this.genes.size() + 1) * fHeight + this.sample2positions.size() * fHeight));
    this.outw.println("\n%%Page: " + count_pages_printed + " " + count_pages_printed);
    this.outw.println("gsave");
    this.outw.println(1.0 + " " + (localPage.height <= this.pageDef.height ? 1.0 : 1.0 / (localPage.getHeight() / (float) this.pageDef.getHeight())) + " scale");
    // this.outw.println( "%%BoundingBox: 0 0 "  + page.width +  " "  + page.height  );
    float midy = (float) (fHeight / 2.0f);
    double cdsHeight = fHeight * 0.4;
    double exonHeight = fHeight * 0.9;
    this.outw.println("2 " + (localPage.height - 10) + " moveto (" + first.getContig() + ":" + this.chromStart + "-" + this.chromEnd + ") show");
    this.outw.println("1 0 0 setrgbcolor");
    this.outw.println("0.3 setlinewidth");
    for (Integer r : this.positions) {
        this.outw.print("newpath " + (float) toPixel(r) + " 0 moveto 0 " + localPage.height + " rlineto stroke\n");
        this.outw.print((float) toPixel(r) + " " + (localPage.height - 5) + " moveto -90 rotate (" + (r) + ") show 90 rotate\n");
    }
    for (int i = 0; i < this.genes.size(); ++i) {
        final Transcript g = this.genes.get(i);
        this.outw.println("gsave");
        this.outw.println("0 " + (localPage.height - margin.top - (fHeight * i)) + " translate");
        double x1 = toPixel(g.getTxStart());
        double x2 = toPixel(g.getTxEnd());
        this.outw.print("0 0 0 setrgbcolor\n");
        NEWPATH();
        MOVETO(x1, midy);
        LINETO(x2, midy);
        STROKE();
        // draw ticks
        this.outw.print("0.2 setlinewidth\n");
        this.outw.print("newpath\n");
        this.outw.print(x1 + " " + midy + " moveto\n");
        this.outw.print(x1 + " " + x2 + (g.isPositiveStrand() ? " forticksF" : " forticksR") + "\n");
        this.outw.print("closepath stroke\n");
        this.outw.print("0.5 setlinewidth\n");
        if (g.hasCodonStartDefined() && g.hasCodonStopDefined()) {
            // draw txStart/txEnd
            this.outw.print("0.1 0.1 0.5 setrgbcolor\n" + "newpath\n" + +toPixel(g.getCodonStart().get().getStart()) + " " + +(midy - cdsHeight / 2.0) + " " + (toPixel(g.getCodonStop().get().getEnd()) - toPixel(g.getEnd())) + " " + cdsHeight + " box closepath fill\n");
        }
        // draw each exon
        for (int j = 0; j < g.getExonCount(); ++j) {
            this.outw.print(toPixel(g.getExon(j).getStart()) + " " + (midy - exonHeight / 2.0) + " " + (float) (toPixel(g.getExon(j).getEnd()) - toPixel(g.getExon(j).getStart())) + " " + exonHeight + " gradient\n");
        }
        // draw name
        this.outw.print("0 0 0 setrgbcolor\n");
        this.outw.print("10 " + midy + " moveto (" + g.getId() + ") show\n");
        this.outw.println("grestore");
    }
    // samples
    {
        double y = localPage.height - margin.top - (fHeight * (this.genes.size() + 1));
        for (String sample : this.sample2positions.keySet()) {
            this.outw.print("0.2 setlinewidth\n");
            this.outw.print("0 0 0 setrgbcolor\n");
            this.outw.print("10 " + (y - midy + 5) + " moveto (" + sample + ") show\n");
            this.outw.print("newpath " + margin.left + " " + y + " moveto\n" + pageDef.width + " " + 0 + " rlineto stroke\n");
            for (Integer r2 : this.sample2positions.get(sample)) {
                this.outw.print("0.8 setlinewidth\n");
                this.outw.print("newpath " + toPixel(r2) + " " + y + " circle closepath stroke\n");
            }
            y -= fHeight;
        }
    }
    this.outw.println("grestore");
    this.outw.print("showpage\n");
}

Example 20 with Transcript

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

the class BackLocate method doWork.

@Override
public int doWork(final List<String> args) {
    PrintStream out = null;
    BufferedReader in = null;
    try {
        this.referenceGenome = ReferenceSequenceFileFactory.getReferenceSequenceFile(this.faidx);
        try (GtfReader gtfReader = new GtfReader(this.gtfPath)) {
            final SAMSequenceDictionary dict = SequenceDictionaryUtils.extractRequired(this.referenceGenome);
            final ContigNameConverter contigNameConverter = ContigNameConverter.fromOneDictionary(dict);
            gtfReader.setContigNameConverter(contigNameConverter);
            gtfReader.getAllGenes().stream().filter(G -> !StringUtils.isBlank(G.getGeneName())).flatMap(G -> G.getTranscripts().stream()).filter(T -> T.isCoding() && T.hasCDS()).forEach(T -> {
                final String gn = T.getGene().getGeneName().toUpperCase();
                List<Transcript> L = this.name2transcripts.get(gn);
                if (L == null) {
                    L = new ArrayList<>();
                    this.name2transcripts.put(gn, L);
                }
                L.add(T);
            });
        }
        out = this.openPathOrStdoutAsPrintStream(this.outputFile);
        out.print("#User.Gene");
        out.print('\t');
        out.print("AA1");
        out.print('\t');
        out.print("petide.pos.1");
        out.print('\t');
        out.print("AA2");
        out.print('\t');
        out.print("transcript.name");
        out.print('\t');
        out.print("transcript.id");
        out.print('\t');
        out.print("transcript.strand");
        out.print('\t');
        out.print("transcript.AA");
        out.print('\t');
        out.print("index0.in.rna");
        out.print('\t');
        out.print("wild.codon");
        out.print('\t');
        out.print("potential.var.codons");
        out.print('\t');
        out.print("base.in.rna");
        out.print('\t');
        out.print("chromosome");
        out.print('\t');
        out.print("index0.in.genomic");
        out.print('\t');
        out.print("exon");
        if (this.printSequences) {
            out.print('\t');
            out.print("mRNA");
            out.print('\t');
            out.print("protein");
        }
        out.print('\t');
        out.print("messages");
        out.print('\t');
        out.print("extra.user.data");
        out.println();
        if (args.isEmpty()) {
            in = super.openBufferedReader(null);
            this.run(out, in);
            CloserUtil.close(in);
        } else {
            for (final String filename : args) {
                in = super.openBufferedReader(filename);
                this.run(out, in);
                CloserUtil.close(in);
            }
        }
        return 0;
    } catch (final Exception e) {
        LOG.severe(e);
        return -1;
    } finally {
        CloserUtil.close(this.referenceGenome);
        this.referenceGenome = null;
        CloserUtil.close(out);
        CloserUtil.close(in);
    }
}