Examples with BioSequence ubic.gemma.model.genome.biosequence.BioSequence used on opensource projects

Example 36 with BioSequence

use of ubic.gemma.model.genome.biosequence.BioSequence in project Gemma by PavlidisLab.

the class ProbeSequenceParser method parseOneLine.

@Override
public BioSequence parseOneLine(String line) {
    if (line.startsWith(">")) {
        throw new RuntimeException("FASTA format not supported - please use the tabular format for oligonucleotides");
    }
    if (StringUtils.isBlank(line)) {
        return null;
    }
    String[] sArray = StringUtils.splitPreserveAllTokens(line);
    if (sArray.length == 0) {
        return null;
    }
    if (sArray.length != 3) {
        throw new IllegalArgumentException("Expected 3 fields: probe name, sequence name, sequence; line=" + line);
    }
    String probeId = sArray[0].trim();
    if (StringUtils.isBlank(probeId)) {
        return null;
    }
    String sequenceName = sArray[1].trim();
    String sequence = sArray[2].trim();
    // Rarely there are extra junk characters. See bug 2719
    sequence = sequence.replaceAll("[^a-yA-Y]", "");
    if (StringUtils.isBlank(sequence)) {
        return null;
    }
    BioSequence seq = BioSequence.Factory.newInstance();
    seq.setSequence(sequence);
    seq.setLength((long) sequence.length());
    seq.setIsCircular(false);
    seq.setIsApproximateLength(false);
    seq.setName(sequenceName);
    if (this.results.containsKey(probeId)) {
        log.warn("Duplicated probe id: " + probeId);
    }
    this.put(probeId, seq);
    return seq;
}

Example 37 with BioSequence

use of ubic.gemma.model.genome.biosequence.BioSequence in project Gemma by PavlidisLab.

the class DesignElementDataVectorDaoImpl method thaw.

@Override
public void thaw(T designElementDataVector) {
    Session session = this.getHibernateTemplate().getSessionFactory().getCurrentSession();
    BioSequence seq = designElementDataVector.getDesignElement().getBiologicalCharacteristic();
    if (seq != null) {
        session.buildLockRequest(LockOptions.NONE).lock(seq);
        Hibernate.initialize(seq);
    }
    ArrayDesign arrayDesign = designElementDataVector.getDesignElement().getArrayDesign();
    Hibernate.initialize(arrayDesign);
    // thawRawAndProcessed the bioassays.
    for (BioAssay ba : designElementDataVector.getBioAssayDimension().getBioAssays()) {
        ba = (BioAssay) session.get(BioAssay.class, ba.getId());
        Hibernate.initialize(ba.getArrayDesignUsed());
        Hibernate.initialize(ba.getSampleUsed());
        Hibernate.initialize(ba.getDerivedDataFiles());
    }
}

Example 38 with BioSequence

use of ubic.gemma.model.genome.biosequence.BioSequence in project Gemma by PavlidisLab.

the class CompositeSequenceDaoImpl method thaw.

@Override
public void thaw(final Collection<CompositeSequence> compositeSequences) {
    HibernateTemplate templ = this.getHibernateTemplate();
    templ.executeWithNativeSession(new org.springframework.orm.hibernate3.HibernateCallback<Object>() {

        @Override
        public Object doInHibernate(org.hibernate.Session session) throws org.hibernate.HibernateException {
            int i = 0;
            int numToDo = compositeSequences.size();
            for (CompositeSequence cs : compositeSequences) {
                session.buildLockRequest(LockOptions.NONE).lock(cs);
                Hibernate.initialize(cs.getArrayDesign());
                BioSequence bs = cs.getBiologicalCharacteristic();
                if (bs == null) {
                    continue;
                }
                session.buildLockRequest(LockOptions.NONE).lock(bs);
                Hibernate.initialize(bs);
                Hibernate.initialize(bs.getTaxon());
                DatabaseEntry dbEntry = bs.getSequenceDatabaseEntry();
                if (dbEntry != null) {
                    Hibernate.initialize(dbEntry);
                    Hibernate.initialize(dbEntry.getExternalDatabase());
                    session.evict(dbEntry);
                    session.evict(dbEntry.getExternalDatabase());
                }
                if (bs.getBioSequence2GeneProduct() == null) {
                    continue;
                }
                for (BioSequence2GeneProduct bs2gp : bs.getBioSequence2GeneProduct()) {
                    if (bs2gp == null) {
                        continue;
                    }
                    GeneProduct geneProduct = bs2gp.getGeneProduct();
                    if (geneProduct != null && geneProduct.getGene() != null) {
                        Gene g = geneProduct.getGene();
                        g.getAliases().size();
                        session.evict(g);
                        session.evict(geneProduct);
                    }
                }
                if (++i % 2000 == 0) {
                    AbstractDao.log.info("Progress: " + i + "/" + numToDo + "...");
                    try {
                        Thread.sleep(10);
                    } catch (InterruptedException e) {
                    // 
                    }
                }
                session.evict(bs);
            }
            session.clear();
            return null;
        }
    });
}

Example 39 with BioSequence

use of ubic.gemma.model.genome.biosequence.BioSequence in project Gemma by PavlidisLab.

the class CompositeSequenceServiceImpl method getGeneMappingSummary.

@Override
public Collection<GeneMappingSummary> getGeneMappingSummary(CompositeSequence cs) {
    BioSequence biologicalCharacteristic = cs.getBiologicalCharacteristic();
    biologicalCharacteristic = bioSequenceService.thaw(biologicalCharacteristic);
    Map<Integer, GeneMappingSummary> results = new HashMap<>();
    if (biologicalCharacteristic == null || biologicalCharacteristic.getBioSequence2GeneProduct() == null) {
        return results.values();
    }
    Collection<BioSequence2GeneProduct> bs2gps = biologicalCharacteristic.getBioSequence2GeneProduct();
    for (BioSequence2GeneProduct bs2gp : bs2gps) {
        GeneProductValueObject geneProduct = new GeneProductValueObject(geneProductService.thaw(bs2gp.getGeneProduct()));
        GeneValueObject gene = new GeneValueObject(bs2gp.getGeneProduct().getGene());
        BlatResultValueObject blatResult = null;
        if ((bs2gp instanceof BlatAssociation)) {
            BlatAssociation blatAssociation = (BlatAssociation) bs2gp;
            blatResult = new BlatResultValueObject(blatResultService.thaw(blatAssociation.getBlatResult()));
        } else if (bs2gp instanceof AnnotationAssociation) {
            /*
                 * Make a dummy blat result
                 */
            blatResult = new BlatResultValueObject();
            blatResult.setQuerySequence(BioSequenceValueObject.fromEntity(biologicalCharacteristic));
            blatResult.setId(biologicalCharacteristic.getId());
        }
        if (blatResult == null) {
            continue;
        }
        if (results.containsKey(ProbeMapUtils.hashBlatResult(blatResult))) {
            results.get(ProbeMapUtils.hashBlatResult(blatResult)).addGene(geneProduct, gene);
        } else {
            GeneMappingSummary summary = new GeneMappingSummary();
            summary.addGene(geneProduct, gene);
            summary.setBlatResult(blatResult);
            summary.setCompositeSequence(this.loadValueObject(cs));
            results.put(ProbeMapUtils.hashBlatResult(blatResult), summary);
        }
    }
    this.addBlatResultsLackingGenes(cs, results);
    if (results.size() == 0) {
        // add a 'dummy' that at least contains the information about the CS. This is a bit of a hack...
        GeneMappingSummary summary = new GeneMappingSummary();
        summary.setCompositeSequence(this.loadValueObject(cs));
        BlatResultValueObject newInstance = new BlatResultValueObject(-1L);
        newInstance.setQuerySequence(BioSequenceValueObject.fromEntity(biologicalCharacteristic));
        summary.setBlatResult(newInstance);
        results.put(ProbeMapUtils.hashBlatResult(newInstance), summary);
    }
    return results.values();
}

Example 40 with BioSequence

use of ubic.gemma.model.genome.biosequence.BioSequence in project Gemma by PavlidisLab.

the class CompositeSequenceServiceImpl method addBlatResultsLackingGenes.

/**
 * Note that duplicate hits will be ignored here. See bug 4037.
 */
private void addBlatResultsLackingGenes(CompositeSequence cs, Map<Integer, GeneMappingSummary> blatResults) {
    /*
         * Pick up blat results that didn't map to genes.
         */
    BioSequence biologicalCharacteristic = bioSequenceService.thaw(cs.getBiologicalCharacteristic());
    Collection<BlatResultValueObject> allBlatResultsForCs = blatResultService.loadValueObjects(blatResultService.thaw(blatResultService.findByBioSequence(biologicalCharacteristic)));
    for (BlatResultValueObject blatResult : allBlatResultsForCs) {
        if (!blatResults.containsKey(ProbeMapUtils.hashBlatResult(blatResult))) {
            GeneMappingSummary summary = new GeneMappingSummary();
            summary.setBlatResult(blatResult);
            summary.setCompositeSequence(this.loadValueObject(cs));
            // no gene...
            blatResults.put(ProbeMapUtils.hashBlatResult(blatResult), summary);
        }
    }
}