Examples with CompositeSequenceService ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService used on opensource projects

Example 1 with CompositeSequenceService

use of ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService 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 2 with CompositeSequenceService

use of ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService in project Gemma by PavlidisLab.

the class GenericGenelistDesignGenerator method processOptions.

@Override
protected void processOptions() {
    super.processOptions();
    geneService = this.getBean(GeneService.class);
    arrayDesignAnnotationService = this.getBean(ArrayDesignAnnotationService.class);
    TaxonService taxonService = this.getBean(TaxonService.class);
    bioSequenceService = this.getBean(BioSequenceService.class);
    arrayDesignService = this.getBean(ArrayDesignService.class);
    compositeSequenceService = this.getBean(CompositeSequenceService.class);
    annotationAssociationService = this.getBean(AnnotationAssociationService.class);
    externalDatabaseService = this.getBean(ExternalDatabaseService.class);
    arrayDesignReportService = this.getBean(ArrayDesignReportService.class);
    if (this.hasOption('t')) {
        this.taxon = this.setTaxonByName(taxonService);
    }
    if (this.hasOption("ncbiids")) {
        this.useNCBIIds = true;
    } else if (this.hasOption("ensembl")) {
        this.useEnsemblIds = true;
    }
    if (useNCBIIds && useEnsemblIds) {
        throw new IllegalArgumentException("Choose one of ensembl or ncbi ids or gene symbols");
    }
}