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

Example 1 with ArrayDesignSequenceAlignmentService

use of ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceAlignmentService 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 ArrayDesignSequenceAlignmentService

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

the class ArrayDesignBlatCli method processOptions.

@Override
protected void processOptions() {
    super.processOptions();
    if (this.hasOption("sensitive")) {
        this.sensitive = true;
    }
    if (this.hasOption('b')) {
        this.blatResultFile = this.getOptionValue('b');
    }
    if (this.hasOption(AbstractCLI.THREADS_OPTION)) {
        this.numThreads = this.getIntegerOptionValue("threads");
    }
    if (this.hasOption('s')) {
        this.blatScoreThreshold = this.getDoubleOptionValue('s');
    }
    TaxonService taxonService = this.getBean(TaxonService.class);
    if (this.hasOption('t')) {
        String taxonName = this.getOptionValue('t');
        this.taxon = taxonService.findByCommonName(taxonName);
        if (taxon == null) {
            throw new IllegalArgumentException("No taxon named " + taxonName);
        }
    }
    arrayDesignSequenceAlignmentService = this.getBean(ArrayDesignSequenceAlignmentService.class);
}