Examples with BlatAssociation ubic.gemma.model.genome.sequenceAnalysis.BlatAssociation used on opensource projects

Example 1 with BlatAssociation

use of ubic.gemma.model.genome.sequenceAnalysis.BlatAssociation in project Gemma by PavlidisLab.

the class ProbeMapperTest method testProcessBlatResults.

public void testProcessBlatResults() {
    ProbeMapperConfig config = new ProbeMapperConfig();
    // test is sensitive to this.
    config.setMinimumExonOverlapFraction(0);
    ProbeMapper pm = new ProbeMapperImpl();
    Map<String, Collection<BlatAssociation>> res = pm.processBlatResults(mousegp, blatres, config);
    TestCase.assertTrue("No results", res.values().size() > 0);
    TestCase.assertTrue("No results", res.values().iterator().next().size() > 0);
    boolean found = false;
    for (Collection<BlatAssociation> r : res.values()) {
        for (BlatAssociation blatAssociation : r) {
            if ("Filip1l".equals(blatAssociation.getGeneProduct().getGene().getOfficialSymbol())) {
                found = true;
            }
        }
    }
    TestCase.assertTrue(found);
}

Example 2 with BlatAssociation

use of ubic.gemma.model.genome.sequenceAnalysis.BlatAssociation in project Gemma by PavlidisLab.

the class ArrayDesignMapResultServiceImpl method summarizeMapResults.

@Override
public Collection<CompositeSequenceMapSummary> summarizeMapResults(Collection<CompositeSequence> compositeSequences) {
    Collection<CompositeSequenceMapSummary> result = new HashSet<>();
    int count = 0;
    for (CompositeSequence cs : compositeSequences) {
        CompositeSequenceMapSummary summary = new CompositeSequenceMapSummary(cs);
        BioSequence bioSequence = cs.getBiologicalCharacteristic();
        if (bioSequence == null) {
            result.add(summary);
            continue;
        }
        Collection<BlatResult> blats = blatResultService.findByBioSequence(bioSequence);
        summary.setBlatResults(blats);
        Collection<BlatAssociation> maps = blatAssociationService.find(bioSequence);
        blatAssociationService.thaw(maps);
        for (BlatAssociation association : maps) {
            summary.getGeneProducts().add(association.getGeneProduct());
            summary.getGenes().add(association.getGeneProduct().getGene());
        }
        result.add(summary);
        if (++count % 1000 == 0) {
            ArrayDesignMapResultServiceImpl.log.info("Processed " + count + " elements...");
        }
    }
    ArrayDesignMapResultServiceImpl.log.info("Done, processed " + count + " elements");
    return result;
}

Example 3 with BlatAssociation

use of ubic.gemma.model.genome.sequenceAnalysis.BlatAssociation in project Gemma by PavlidisLab.

the class ArrayDesignProbeMapperCli method processProbes.

private void processProbes(ArrayDesign arrayDesign) {
    assert this.probeNames != null && this.probeNames.length > 0;
    arrayDesign = arrayDesignService.thawLite(arrayDesign);
    CompositeSequenceService compositeSequenceService = this.getBean(CompositeSequenceService.class);
    for (String probeName : this.probeNames) {
        CompositeSequence probe = compositeSequenceService.findByName(arrayDesign, probeName);
        if (probe == null) {
            AbstractCLI.log.warn("No such probe: " + probeName + " on " + arrayDesign.getShortName());
            continue;
        }
        probe = compositeSequenceService.thaw(probe);
        Map<String, Collection<BlatAssociation>> results = this.arrayDesignProbeMapperService.processCompositeSequence(this.config, taxon, null, probe);
        for (Collection<BlatAssociation> col : results.values()) {
            for (BlatAssociation association : col) {
                if (AbstractCLI.log.isDebugEnabled())
                    AbstractCLI.log.debug(association);
            }
            arrayDesignProbeMapperService.printResult(probe, col);
        }
    }
}

Example 4 with BlatAssociation

use of ubic.gemma.model.genome.sequenceAnalysis.BlatAssociation in project Gemma by PavlidisLab.

the class GoldenPathSequenceAnalysis method findAssociations.

/**
 * Given a physical location, identify overlapping genes or predicted genes.
 *
 * @param chromosome The chromosome name (the organism is set by the constructor)
 * @param queryStart The start base of the region to query (the start of the alignment to the genome)
 * @param queryEnd The end base of the region to query (the end of the alignment to the genome)
 * @param starts Locations of alignment block starts in target. (comma-delimited from blat)
 * @param sizes Sizes of alignment blocks (comma-delimited from blat)
 * @param strand Either + or - indicating the strand to look on, or null to search both strands.
 * @param method The constant representing the method to use to locate the 3' distance.
 * @param config configuration
 * @return A list of BioSequence2GeneProduct objects. The distance stored by a ThreePrimeData will be 0 if the
 *         sequence overhangs the found genes (rather than providing a negative distance). If no genes are found,
 *         the result is null; These are transient instances, not from Gemma's database
 */
public Collection<BlatAssociation> findAssociations(String chromosome, Long queryStart, Long queryEnd, String starts, String sizes, String strand, ThreePrimeDistanceMethod method, ProbeMapperConfig config) {
    if (GoldenPath.log.isDebugEnabled())
        GoldenPath.log.debug("Seeking gene overlaps with: chrom=" + chromosome + " start=" + queryStart + " end=" + queryEnd + " strand=" + strand);
    if (queryEnd < queryStart)
        throw new IllegalArgumentException("End must not be less than start");
    /*
         * These are transient instances only
         */
    Collection<GeneProduct> geneProducts = new HashSet<>();
    if (config.isUseRefGene()) {
        // starting with refgene means we can get the correct transcript name etc.
        geneProducts.addAll(this.findRefGenesByLocation(chromosome, queryStart, queryEnd, strand));
    }
    if (config.isUseKnownGene()) {
        // get known genes as well, in case all we got was an intron. Currently does not work with rat (rn6)
        geneProducts.addAll(this.findKnownGenesByLocation(chromosome, queryStart, queryEnd, strand));
    }
    if (geneProducts.size() == 0)
        return null;
    Collection<BlatAssociation> results = new HashSet<>();
    for (GeneProduct geneProduct : geneProducts) {
        if (GoldenPath.log.isDebugEnabled())
            GoldenPath.log.debug(geneProduct);
        BlatAssociation blatAssociation = this.computeLocationInGene(chromosome, queryStart, queryEnd, starts, sizes, geneProduct, method, config);
        /*
             * We check against the actual threshold later. We can't fully check it now because not all the slots are
             * populated yet.
             */
        if (config.getMinimumExonOverlapFraction() > 0.0 && blatAssociation.getOverlap() == 0) {
            GoldenPath.log.debug("Result failed to meet exon overlap threshold (0)");
            continue;
        }
        results.add(blatAssociation);
    }
    return results;
}

Example 5 with BlatAssociation

use of ubic.gemma.model.genome.sequenceAnalysis.BlatAssociation in project Gemma by PavlidisLab.

the class BlatAssociationScorer method organizeBlatAssociationsByGene.

private static Map<Gene, Collection<BlatAssociation>> organizeBlatAssociationsByGene(Collection<BlatAssociation> blatAssociations) {
    Map<Gene, Collection<BlatAssociation>> genes = new HashMap<>();
    for (BlatAssociation blatAssociation : blatAssociations) {
        Gene gene = blatAssociation.getGeneProduct().getGene();
        if (!genes.containsKey(gene)) {
            genes.put(gene, new HashSet<BlatAssociation>());
        }
        genes.get(gene).add(blatAssociation);
    }
    return genes;
}