Examples with ArrayDesignProbeMapperService ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignProbeMapperService used on opensource projects

Example 1 with ArrayDesignProbeMapperService

use of ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignProbeMapperService in project Gemma by PavlidisLab.

the class CompositeSequenceGeneMapperServiceTest method blatCollapsedSequences.

private void blatCollapsedSequences() throws IOException {
    Taxon taxon = taxonService.findByScientificName("Homo sapiens");
    ArrayDesignSequenceAlignmentService aligner = this.getBean(ArrayDesignSequenceAlignmentService.class);
    InputStream blatResultInputStream = new GZIPInputStream(this.getClass().getResourceAsStream("/data/loader/genome/gpl96.blatresults.psl.gz"));
    Collection<BlatResult> results = blat.processPsl(blatResultInputStream, taxon);
    aligner.processArrayDesign(ad, taxon, results);
    // real stuff.
    ArrayDesignProbeMapperService arrayDesignProbeMapperService = this.getBean(ArrayDesignProbeMapperService.class);
    arrayDesignProbeMapperService.processArrayDesign(ad);
}

Example 2 with ArrayDesignProbeMapperService

use of ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignProbeMapperService in project Gemma by PavlidisLab.

the class ArrayDesignProbeMapperCli method processOptions.

/**
 * See 'configure' for how the other options are handled. (non-Javadoc)
 *
 * @see ArrayDesignSequenceManipulatingCli#processOptions()
 */
@Override
protected void processOptions() {
    super.processOptions();
    arrayDesignProbeMapperService = this.getBean(ArrayDesignProbeMapperService.class);
    TaxonService taxonService = this.getBean(TaxonService.class);
    if (this.hasOption(AbstractCLI.THREADS_OPTION)) {
        this.numThreads = this.getIntegerOptionValue("threads");
    }
    if (this.hasOption("import")) {
        if (!this.hasOption('t')) {
            throw new IllegalArgumentException("You must provide the taxon when using the import option");
        }
        if (!this.hasOption("source")) {
            throw new IllegalArgumentException("You must provide source database name when using the import option");
        }
        String sourceDBName = this.getOptionValue("source");
        ExternalDatabaseService eds = this.getBean(ExternalDatabaseService.class);
        this.sourceDatabase = eds.findByName(sourceDBName);
        this.directAnnotationInputFileName = this.getOptionValue("import");
        if (this.hasOption("ncbi")) {
            this.ncbiIds = true;
        }
    }
    if (this.hasOption('t')) {
        this.taxon = this.setTaxonByName(taxonService);
    }
    if (this.hasOption("nodb")) {
        this.useDB = false;
    }
    if (this.hasOption("probes")) {
        if (this.arrayDesignsToProcess == null || this.arrayDesignsToProcess.size() > 1) {
            throw new IllegalArgumentException("With '-probes' you must provide exactly one platform");
        }
        this.useDB = false;
        probeNames = this.getOptionValue("probes").split(",");
        if (probeNames.length == 0) {
            throw new IllegalArgumentException("You must provide at least one probe name when using '-probes'");
        }
    }
}