Examples with GoldenPathSequenceAnalysis ubic.gemma.core.externalDb.GoldenPathSequenceAnalysis used on opensource projects

Example 1 with GoldenPathSequenceAnalysis

use of ubic.gemma.core.externalDb.GoldenPathSequenceAnalysis in project Gemma by PavlidisLab.

the class ProbeMapperTest method setUp.

@Override
protected void setUp() throws Exception {
    super.setUp();
    tester = new ArrayList<>();
    tester.add(400d);
    tester.add(200d);
    tester.add(100d);
    tester.add(50d);
    try (InputStream is = this.getClass().getResourceAsStream("/data/loader/genome/col8a1.blatresults.txt")) {
        BlatResultParser brp = new BlatResultParser();
        Taxon m = Taxon.Factory.newInstance();
        m.setCommonName("mouse");
        brp.setTaxon(m);
        brp.parse(is);
        blatres = brp.getResults();
        assert blatres != null && blatres.size() > 0;
    }
    String databaseHost = Settings.getString("gemma.testdb.host");
    String databaseUser = Settings.getString("gemma.testdb.user");
    String databasePassword = Settings.getString("gemma.testdb.password");
    mousegp = new GoldenPathSequenceAnalysis(3306, Settings.getString("gemma.goldenpath.db.mouse"), databaseHost, databaseUser, databasePassword);
    humangp = new GoldenPathSequenceAnalysis(3306, Settings.getString("gemma.goldenpath.db.human"), databaseHost, databaseUser, databasePassword);
}

Example 2 with GoldenPathSequenceAnalysis

use of ubic.gemma.core.externalDb.GoldenPathSequenceAnalysis in project Gemma by PavlidisLab.

the class ArrayDesignProbeMapperServiceImpl method processArrayDesign.

@Override
public void processArrayDesign(ArrayDesign arrayDesign, ProbeMapperConfig config, boolean useDB) {
    assert config != null;
    if (arrayDesign.getTechnologyType().equals(TechnologyType.NONE)) {
        throw new IllegalArgumentException("Do not use this service to process platforms that do not use an probe-based technology.");
    }
    Collection<Taxon> taxa = arrayDesignService.getTaxa(arrayDesign.getId());
    Taxon taxon = arrayDesign.getPrimaryTaxon();
    if (taxa.size() > 1 && taxon == null) {
        throw new IllegalArgumentException("Array design has sequence from multiple taxa and has no primary taxon set: " + arrayDesign);
    }
    GoldenPathSequenceAnalysis goldenPathDb = new GoldenPathSequenceAnalysis(taxon);
    BlockingQueue<BACS> persistingQueue = new ArrayBlockingQueue<>(ArrayDesignProbeMapperServiceImpl.QUEUE_SIZE);
    AtomicBoolean generatorDone = new AtomicBoolean(false);
    AtomicBoolean loaderDone = new AtomicBoolean(false);
    this.load(persistingQueue, generatorDone, loaderDone, useDB);
    if (useDB) {
        ArrayDesignProbeMapperServiceImpl.log.info("Removing any old associations");
        arrayDesignService.deleteGeneProductAssociations(arrayDesign);
    }
    int count = 0;
    int hits = 0;
    ArrayDesignProbeMapperServiceImpl.log.info("Start processing " + arrayDesign.getCompositeSequences().size() + " probes ...");
    for (CompositeSequence compositeSequence : arrayDesign.getCompositeSequences()) {
        if (compositeSequence.getName().equals("1431126_a_at")) {
            ArrayDesignProbeMapperServiceImpl.log.debug("HERE");
        }
        Map<String, Collection<BlatAssociation>> results = this.processCompositeSequence(config, taxon, goldenPathDb, compositeSequence);
        if (results == null)
            continue;
        for (Collection<BlatAssociation> col : results.values()) {
            for (BlatAssociation association : col) {
                if (ArrayDesignProbeMapperServiceImpl.log.isDebugEnabled())
                    ArrayDesignProbeMapperServiceImpl.log.debug(association);
                persistingQueue.add(new BACS(compositeSequence, association));
            }
            ++hits;
        }
        if (++count % 200 == 0) {
            ArrayDesignProbeMapperServiceImpl.log.info("Processed " + count + " composite sequences" + " with blat results; " + hits + " mappings found.");
        }
    }
    generatorDone.set(true);
    ArrayDesignProbeMapperServiceImpl.log.info("Waiting for loading to complete ...");
    while (!loaderDone.get()) {
        try {
            Thread.sleep(1000);
        } catch (InterruptedException e) {
            throw new RuntimeException(e);
        }
    }
    ArrayDesignProbeMapperServiceImpl.log.info("Processed " + count + " composite sequences with blat results; " + hits + " mappings found.");
    arrayDesignReportService.generateArrayDesignReport(arrayDesign.getId());
    this.deleteOldFiles(arrayDesign);
}

Example 3 with GoldenPathSequenceAnalysis

use of ubic.gemma.core.externalDb.GoldenPathSequenceAnalysis in project Gemma by PavlidisLab.

the class ArrayDesignProbeMapperServiceImpl method processCompositeSequence.

@Override
@Transactional
public Map<String, Collection<BlatAssociation>> processCompositeSequence(ProbeMapperConfig config, Taxon taxon, GoldenPathSequenceAnalysis goldenPathDb, CompositeSequence compositeSequence) {
    BioSequence bs = compositeSequence.getBiologicalCharacteristic();
    if (bs == null)
        return null;
    /*
         * It isn't 100% clear what the right thing to do is. But this seems at least _reasonable_ when there is a
         * mismatch
         */
    if (taxon != null && !bs.getTaxon().equals(taxon)) {
        return null;
    }
    GoldenPathSequenceAnalysis db;
    if (goldenPathDb == null) {
        db = new GoldenPathSequenceAnalysis(bs.getTaxon());
    } else {
        db = goldenPathDb;
    }
    final Collection<BlatResult> blatResults = blatResultService.findByBioSequence(bs);
    ProbeMapUtils.removeDuplicates(blatResults);
    if (blatResults.isEmpty())
        return null;
    return probeMapper.processBlatResults(db, blatResults, config);
}