Examples with CosmicGeneModel com.hartwig.hmftools.common.cosmic.genes.CosmicGeneModel used on opensource projects

Example 1 with CosmicGeneModel

use of com.hartwig.hmftools.common.cosmic.genes.CosmicGeneModel in project hmftools by hartwigmedical.

the class HmfReporterDataLoader method buildFromFiles.

@NotNull
static HmfReporterData buildFromFiles(@NotNull final String cosmicGeneFile, @NotNull final String cosmicFusionFile, @NotNull final String drupFilterFile, @NotNull final String fastaFileLocation) throws IOException {
    final GeneModel panelGeneModel = new GeneModel(HmfGenePanelSupplier.hmfPanelGeneMap());
    final CosmicGeneModel cosmicGeneModel = CosmicGenes.readFromCSV(cosmicGeneFile);
    final CosmicFusionModel cosmicFusionModel = CosmicFusions.readFromCSV(cosmicFusionFile);
    final DrupFilter drupFilter = new DrupFilter(drupFilterFile);
    final MicrosatelliteAnalyzer microsatelliteAnalyzer = ImmutableMicrosatelliteAnalyzer.of(fastaFileLocation);
    return ImmutableHmfReporterData.of(panelGeneModel, cosmicGeneModel, cosmicFusionModel, drupFilter, microsatelliteAnalyzer);
}

Example 2 with CosmicGeneModel

use of com.hartwig.hmftools.common.cosmic.genes.CosmicGeneModel in project hmftools by hartwigmedical.

the class PatientReporterTestUtil method testHmfReporterData.

@NotNull
public static HmfReporterData testHmfReporterData() throws IOException {
    final String drupFilterPath = Resources.getResource("csv").getPath() + File.separator + "drup_genes.csv";
    final String cosmicPath = Resources.getResource("csv").getPath() + File.separator + "cosmic_slice.csv";
    final String fusionPath = Resources.getResource("csv").getPath() + File.separator + "cosmic_gene_fusions.csv";
    final GeneModel geneModel = new GeneModel(HmfGenePanelSupplier.hmfPanelGeneMap());
    final CosmicGeneModel cosmicGeneModel = CosmicGenes.readFromCSV(cosmicPath);
    final CosmicFusionModel cosmicFusionModel = CosmicFusions.readFromCSV(fusionPath);
    final DrupFilter drupFilter = new DrupFilter(drupFilterPath);
    final MicrosatelliteAnalyzer microsatelliteAnalyzer = testMicrosatelliteAnalyzer();
    return ImmutableHmfReporterData.of(geneModel, cosmicGeneModel, cosmicFusionModel, drupFilter, microsatelliteAnalyzer);
}