Examples with Hsp gov.nih.nlm.ncbi.blast.Hsp used on opensource projects

Example 1 with Hsp

use of gov.nih.nlm.ncbi.blast.Hsp in project jvarkit by lindenb.

the class BlastNToSnp method run.

private void run(PrintWriter pw, XMLEventReader r) throws XMLStreamException, JAXBException {
    long numIterations = 0L;
    long numPerfectMath = 0L;
    long numNoHit = 0L;
    pw.print("#query");
    pw.print('\t');
    pw.print("hit");
    pw.print('\t');
    pw.print(("hit-index"));
    pw.print('\t');
    pw.print("hsp-index");
    pw.print('\t');
    pw.print("query-POS");
    pw.print('\t');
    pw.print("hit-POS");
    pw.print('\t');
    pw.print("STRAND");
    pw.print('\t');
    pw.print("REF(hit)");
    pw.print('\t');
    pw.print("ALT(query)");
    pw.print('\t');
    pw.print("blast.align_length");
    pw.print('\t');
    pw.print("blast.hit.var");
    pw.print('\t');
    pw.print("blast.query.var");
    pw.print('\t');
    pw.print("blast.mid.var");
    pw.println();
    for (; ; ) {
        Iteration iter1 = peekIteration(r);
        if (iter1 == null)
            break;
        ++numIterations;
        if (iter1.getIterationHits().getHit().isEmpty()) {
            LOG.info("No hit found for " + iter1.getIterationQueryDef());
            ++numNoHit;
            continue;
        }
        boolean found_mismatch = false;
        for (int hit_loop = 0; hit_loop < iter1.getIterationHits().getHit().size(); ++hit_loop) {
            final Hit hit = iter1.getIterationHits().getHit().get(hit_loop);
            for (int hsp_loop = 0; hsp_loop < hit.getHitHsps().getHsp().size(); ++hsp_loop) {
                final Hsp hsp = hit.getHitHsps().getHsp().get(hsp_loop);
                String hspQseq = hsp.getHspQseq();
                String hspMid = hsp.getHspMidline();
                String hspHSeq = hsp.getHspHseq();
                int hsp_query_from = Integer.parseInt(hsp.getHspQueryFrom());
                int hsp_query_to = Integer.parseInt(hsp.getHspQueryTo());
                int hsp_hit_from = Integer.parseInt(hsp.getHspHitFrom());
                int hsp_hit_to = Integer.parseInt(hsp.getHspHitTo());
                final int align_length = Integer.parseInt(hsp.getHspAlignLen());
                final int hit_shift = (hsp_hit_from > hsp_hit_to ? -1 : 1);
                int i = 0;
                int query_index = hsp_query_from;
                int hit_index = hsp_hit_from;
                while (i < align_length) {
                    char ch = hspHSeq.charAt(i);
                    char cq = hspQseq.charAt(i);
                    char cm = hspMid.charAt(i);
                    if (cm == '|') {
                        ++i;
                        query_index++;
                        hit_index += hit_shift;
                        continue;
                    }
                    found_mismatch = true;
                    int j = i + 1;
                    for (; ; ) {
                        int k = hspMid.indexOf(' ', j);
                        if (k == -1 || k - j > minGapSize)
                            break;
                        j = k + 1;
                    }
                    String ref = new String(hspHSeq.substring(i, j)).replaceAll("[\\- ]", "");
                    String alt = new String(hspQseq.substring(i, j)).replaceAll("[\\- ]", "");
                    if (hit_shift < 0) {
                        StringBuilder sb = new StringBuilder(alt.length());
                        for (int x = alt.length() - 1; x >= 0; --x) {
                            sb.append(AcidNucleics.complement(alt.charAt(x)));
                        }
                        alt = sb.toString();
                        sb = new StringBuilder(ref.length());
                        for (int x = ref.length() - 1; x >= 0; --x) {
                            sb.append(AcidNucleics.complement(ref.charAt(x)));
                        }
                        ref = sb.toString();
                    }
                    pw.print(iter1.getIterationQueryDef());
                    pw.print('\t');
                    pw.print(hit.getHitDef());
                    pw.print('\t');
                    pw.print((1 + hit_loop));
                    pw.print('\t');
                    pw.print((1 + hsp_loop));
                    pw.print('\t');
                    pw.print(query_index);
                    pw.print('\t');
                    pw.print(hit_index);
                    pw.print('\t');
                    pw.print(hit_shift == 1 ? '+' : '-');
                    pw.print('\t');
                    pw.print(ref);
                    pw.print('\t');
                    pw.print(alt);
                    pw.print('\t');
                    pw.print(align_length);
                    pw.print('\t');
                    pw.print(hspHSeq.substring(i, j).replace(' ', '.'));
                    pw.print('\t');
                    pw.print(hspQseq.substring(i, j).replace(' ', '.'));
                    pw.print('\t');
                    pw.print(hspMid.substring(i, j).replace(' ', '.'));
                    pw.println();
                    while (i < j) {
                        ch = hspHSeq.charAt(i);
                        cq = hspQseq.charAt(i);
                        if (ch != '-' && ch != ' ') {
                            hit_index += hit_shift;
                        }
                        if (cq != '-' && cq != ' ') {
                            query_index++;
                        }
                        ++i;
                    }
                }
                if (hit_index - hit_shift != hsp_hit_to) {
                    marshaller.marshal(new JAXBElement<Hsp>(new QName("Hsp"), Hsp.class, hsp), stderr());
                    throw new IllegalStateException("Error expected hit-index= " + hit_index + "-" + hit_shift + " == hsp-hit-to=" + hsp_hit_to);
                }
                if (query_index - 1 != hsp_query_to) {
                    marshaller.marshal(new JAXBElement<Hit>(new QName("Hit"), Hit.class, hit), stderr());
                    throw new IllegalStateException("query_index " + query_index + "(1 != hsp_query_to:" + hsp_query_to);
                }
                if (pw.checkError())
                    break;
            }
        }
        if (!found_mismatch) {
            numPerfectMath++;
        }
    }
    // end while read
    LOG.info("ITERATIONS : " + numIterations);
    LOG.info("ONLY_PERFECT_MATCH : " + numPerfectMath);
    LOG.info("NO_HIT : " + numNoHit);
}

Example 2 with Hsp

use of gov.nih.nlm.ncbi.blast.Hsp in project jvarkit by lindenb.

the class BlastMapAnnotations method printUniprot.

private void printUniprot(Uniprot uniprotSet) {
    if (uniprotSet.getEntry().isEmpty()) {
        LOG.warn("empty uniprot entry.");
        return;
    }
    if (uniprotSet.getEntry().size() > 1) {
        LOG.warn("entry contains more than one sequence.");
    }
    for (Entry entry : uniprotSet.getEntry()) {
        BlastOutputIterations iterations = this.blastOutput.getBlastOutputIterations();
        for (Iteration iteration : iterations.getIteration()) {
            for (FeatureType feature : entry.getFeature()) {
                if (!acceptfeature(feature.getType()))
                    continue;
                for (Hit hit : iteration.getIterationHits().getHit()) {
                    for (Hsp hsp : hit.getHitHsps().getHsp()) {
                        UniprotInterval bi = new UniprotInterval();
                        bi.entry = entry;
                        bi.featureType = feature;
                        bi.hit = hit;
                        bi.hsp = hsp;
                        LOG.debug("interval " + bi);
                        if (!bi.isFeatureOverlapHsp()) {
                            continue;
                        }
                        stdout().println(bi.toBedString());
                    }
                }
            }
            break;
        }
        break;
    }
// System.err.println("OK");
}

Example 3 with Hsp

use of gov.nih.nlm.ncbi.blast.Hsp in project jvarkit by lindenb.

the class BlastHspAlignment method cloneHsp.

public static Hsp cloneHsp(Hsp hsp) {
    Hsp h2 = new Hsp();
    h2.setHspNum(hsp.getHspNum());
    h2.setHspBitScore(hsp.getHspBitScore());
    h2.setHspScore(hsp.getHspScore());
    h2.setHspEvalue(hsp.getHspEvalue());
    h2.setHspIdentity(hsp.getHspIdentity());
    h2.setHspGaps(hsp.getHspGaps());
    h2.setHspPositive(hsp.getHspPositive());
    h2.setHspAlignLen(hsp.getHspAlignLen());
    h2.setHspQueryFrom(hsp.getHspQueryFrom());
    h2.setHspQueryTo(hsp.getHspQueryTo());
    h2.setHspQueryFrame(hsp.getHspQueryFrame());
    h2.setHspHitFrom(hsp.getHspHitFrom());
    h2.setHspHitTo(hsp.getHspHitTo());
    h2.setHspHitFrame(hsp.getHspHitFrame());
    h2.setHspQseq(hsp.getHspQseq());
    h2.setHspHseq(hsp.getHspHseq());
    h2.setHspMidline(hsp.getHspMidline());
    h2.setHspPatternFrom(hsp.getHspPatternFrom());
    h2.setHspPatternTo(hsp.getHspPatternTo());
    return h2;
}

Example 4 with Hsp

use of gov.nih.nlm.ncbi.blast.Hsp in project jvarkit by lindenb.

the class Biostar3654 method parseIteration.

private void parseIteration(String database, Iteration iteration) throws Exception {
    this.pw.println("QUERY: " + iteration.getIterationQueryDef());
    this.pw.println("       ID:" + iteration.getIterationQueryID() + " Len:" + iteration.getIterationQueryLen());
    for (Hit hit : iteration.getIterationHits().getHit()) {
        this.pw.println(">" + hit.getHitDef());
        this.pw.println(" " + hit.getHitAccession());
        this.pw.println(" id:" + hit.getHitId() + " len:" + hit.getHitLen());
        for (Hsp hsp : hit.getHitHsps().getHsp()) {
            List<INSDFeature> qFeatures = fetchAnnotations(database, iteration.getIterationQueryID(), Integer.parseInt(hsp.getHspQueryFrom()), Integer.parseInt(hsp.getHspQueryTo()));
            List<INSDFeature> hFeatures = fetchAnnotations(database, hit.getHitAccession(), Integer.parseInt(hsp.getHspHitFrom()), Integer.parseInt(hsp.getHspHitTo()));
            this.pw.println();
            this.pw.println("   e-value:" + hsp.getHspEvalue() + " gap:" + hsp.getHspGaps() + " bitScore:" + hsp.getHspBitScore());
            this.pw.println();
            // create the Printer for the Query and the Hit
            QPrinter qPrinter = new QPrinter(hsp, qFeatures);
            HPrinter hPrinter = new HPrinter(hsp, hFeatures);
            // loop over the lines
            while (qPrinter.next() && hPrinter.next()) {
                qPrinter.print();
                this.pw.printf("QUERY %0" + margin + "d ", qPrinter.seqStart);
                this.pw.print(hsp.getHspQseq().substring(qPrinter.stringStart, qPrinter.stringEnd));
                this.pw.printf(" %0" + margin + "d", qPrinter.seqEnd - (qPrinter.sign));
                this.pw.println();
                this.pw.printf("      %" + margin + "s ", "");
                this.pw.print(hsp.getHspMidline().substring(qPrinter.stringStart, qPrinter.stringEnd));
                this.pw.println();
                this.pw.printf("HIT   %0" + margin + "d ", hPrinter.seqStart);
                this.pw.print(hsp.getHspHseq().substring(hPrinter.stringStart, hPrinter.stringEnd));
                this.pw.printf(" %0" + margin + "d", hPrinter.seqEnd - (hPrinter.sign));
                this.pw.println();
                hPrinter.print();
                this.pw.println();
            }
            this.pw.flush();
        }
    }
// System.err.println("OK");
}

Example 5 with Hsp

use of gov.nih.nlm.ncbi.blast.Hsp in project jvarkit by lindenb.

the class MergeSplittedBlast method merge.

private Hit merge(List<Hit> hits) {
    Hit first = hits.get(0);
    Split firstSplit = parse(first);
    Hit newHit = new Hit();
    newHit.setHitAccession(first.getHitAccession());
    newHit.setHitDef(firstSplit.chrom);
    newHit.setHitId(first.getHitId());
    newHit.setHitNum(first.getHitNum());
    newHit.setHitLen(String.valueOf(firstSplit.len));
    newHit.setHitHsps(new HitHsps());
    List<Hsp> hsps = new ArrayList<Hsp>();
    for (Hit h0 : hits) {
        /* fix hit_from/hit_to */
        Split split = parse(h0);
        List<Hsp> L = h0.getHitHsps().getHsp();
        for (int i = 0; i < L.size(); ++i) {
            Hsp newHsp = BlastHspAlignment.cloneHsp(L.get(i));
            BlastHspAlignment aln = new BlastHspAlignment(newHsp);
            int h_from = aln.getHitFrom1();
            int h_to = aln.getHitTo1();
            h_from += (split.start1 - 1);
            h_to += (split.start1 - 1);
            newHsp.setHspHitFrom(String.valueOf(h_from));
            newHsp.setHspHitTo(String.valueOf(h_to));
            hsps.add(newHsp);
        }
    }
    boolean done = false;
    while (!done) {
        done = true;
        for (int i = 0; i + 1 < hsps.size(); ++i) {
            Hsp hsp0 = hsps.get(i);
            for (int j = i + 1; j < hsps.size(); ++j) {
                // debug("comparing hsp "+i+" vs "+j+" N="+hsps.size());
                Hsp hsp1 = hsps.get(j);
                Hsp newHitHsp = merge(hsp0, hsp1);
                if (newHitHsp != null) {
                    hsps.set(i, newHitHsp);
                    hsps.remove(j);
                    done = false;
                    break;
                }
            }
            if (!done)
                break;
        }
    }
    for (int i = 0; i < hsps.size(); ++i) hsps.get(i).setHspNum(String.valueOf(i + 1));
    newHit.getHitHsps().getHsp().addAll(hsps);
    return newHit;
}