Examples with PurityContext com.hartwig.hmftools.common.purple.purity.PurityContext used on opensource projects

Example 1 with PurityContext

use of com.hartwig.hmftools.common.purple.purity.PurityContext in project hmftools by hartwigmedical.

the class LoadPurpleData method main.

public static void main(@NotNull final String[] args) throws ParseException, IOException, SQLException {
    final Options options = createBasicOptions();
    final CommandLine cmd = createCommandLine(args, options);
    final DatabaseAccess dbAccess = databaseAccess(cmd);
    final String tumorSample = cmd.getOptionValue(SAMPLE);
    final String purplePath = cmd.getOptionValue(PURPLE_DIR);
    LOGGER.info("Persisting purity data");
    final PurpleQC purpleQC = PurpleQCFile.read(PurpleQCFile.generateFilename(purplePath, tumorSample));
    final PurityContext purityContext = FittedPurityFile.read(purplePath, tumorSample);
    final List<FittedPurity> bestFitPerPurity = FittedPurityRangeFile.read(purplePath, tumorSample);
    dbAccess.writePurity(tumorSample, purityContext, purpleQC);
    dbAccess.writeBestFitPerPurity(tumorSample, bestFitPerPurity);
    LOGGER.info("Persisting copy numbers");
    final List<PurpleCopyNumber> copyNumbers = PurpleCopyNumberFile.read(purplePath, tumorSample);
    dbAccess.writeCopynumbers(tumorSample, copyNumbers);
    LOGGER.info("Persisting gene copy numbers");
    final List<GeneCopyNumber> geneCopyNumbers = GeneCopyNumberFile.read(GeneCopyNumberFile.generateFilename(purplePath, tumorSample));
    dbAccess.writeGeneCopynumberRegions(tumorSample, geneCopyNumbers);
    LOGGER.info("Complete");
}

Example 2 with PurityContext

use of com.hartwig.hmftools.common.purple.purity.PurityContext in project hmftools by hartwigmedical.

the class LoadSomaticVariants method main.

public static void main(@NotNull final String[] args) throws ParseException, IOException, SQLException {
    final Options options = createBasicOptions();
    final CommandLine cmd = createCommandLine(args, options);
    final String vcfFileLocation = cmd.getOptionValue(VCF_FILE);
    final String highConfidenceBed = cmd.getOptionValue(HIGH_CONFIDENCE_BED);
    final String fastaFileLocation = cmd.getOptionValue(REF_GENOME);
    final String sample = cmd.getOptionValue(SAMPLE);
    final DatabaseAccess dbAccess = databaseAccess(cmd);
    final CompoundFilter filter = new CompoundFilter(true);
    if (cmd.hasOption(PASS_FILTER)) {
        filter.add(new PassingVariantFilter());
    }
    if (cmd.hasOption(SOMATIC_FILTER)) {
        filter.add(new SomaticFilter());
    }
    LOGGER.info("Reading somatic VCF File");
    final List<SomaticVariant> variants = SomaticVariantFactory.filteredInstance(filter).fromVCFFile(sample, vcfFileLocation);
    LOGGER.info("Reading high confidence bed file");
    final Multimap<String, GenomeRegion> highConfidenceRegions = BEDFileLoader.fromBedFile(highConfidenceBed);
    LOGGER.info("Loading indexed fasta reference file");
    IndexedFastaSequenceFile indexedFastaSequenceFile = new IndexedFastaSequenceFile(new File(fastaFileLocation));
    LOGGER.info("Querying purple database");
    final PurityContext purityContext = dbAccess.readPurityContext(sample);
    if (purityContext == null) {
        LOGGER.warn("Unable to retrieve purple data. Enrichment may be incomplete.");
    }
    final PurityAdjuster purityAdjuster = purityContext == null ? new PurityAdjuster(Gender.FEMALE, 1, 1) : new PurityAdjuster(purityContext.gender(), purityContext.bestFit().purity(), purityContext.bestFit().normFactor());
    final Multimap<String, PurpleCopyNumber> copyNumbers = Multimaps.index(dbAccess.readCopynumbers(sample), PurpleCopyNumber::chromosome);
    final Multimap<String, FittedRegion> copyNumberRegions = Multimaps.index(dbAccess.readCopyNumberRegions(sample), FittedRegion::chromosome);
    LOGGER.info("Incorporating purple purity");
    final PurityAdjustedSomaticVariantFactory purityAdjustmentFactory = new PurityAdjustedSomaticVariantFactory(purityAdjuster, copyNumbers, copyNumberRegions);
    final List<PurityAdjustedSomaticVariant> purityAdjustedVariants = purityAdjustmentFactory.create(variants);
    final double clonalPloidy = ClonalityCutoffKernel.clonalCutoff(purityAdjustedVariants);
    LOGGER.info("Enriching variants");
    final EnrichedSomaticVariantFactory enrichedSomaticVariantFactory = new EnrichedSomaticVariantFactory(highConfidenceRegions, indexedFastaSequenceFile, new ClonalityFactory(purityAdjuster, clonalPloidy), CanonicalTranscriptFactory.create(HmfGenePanelSupplier.allGeneList()));
    final List<EnrichedSomaticVariant> enrichedVariants = enrichedSomaticVariantFactory.enrich(purityAdjustedVariants);
    LOGGER.info("Persisting variants to database");
    dbAccess.writeSomaticVariants(sample, enrichedVariants);
    LOGGER.info("Complete");
}

Example 3 with PurityContext

use of com.hartwig.hmftools.common.purple.purity.PurityContext in project hmftools by hartwigmedical.

the class PatientReporter method analyseGenomeData.

@NotNull
private GenomeAnalysis analyseGenomeData(@NotNull final String sample, @NotNull final String runDirectory) throws IOException {
    LOGGER.info(" Loading somatic snv and indels...");
    final List<SomaticVariant> variants = PatientReporterHelper.loadPassedSomaticVariants(sample, runDirectory);
    LOGGER.info("  " + variants.size() + " somatic passed snps, mnps and indels loaded for sample " + sample);
    LOGGER.info(" Analyzing somatic snp/mnp and indels....");
    final VariantAnalysis variantAnalysis = variantAnalyzer().run(variants);
    LOGGER.info(" Loading purity numbers...");
    final PurityContext context = PatientReporterHelper.loadPurity(runDirectory, sample);
    if (context.status().equals(FittedPurityStatus.NO_TUMOR)) {
        LOGGER.warn("PURPLE DID NOT DETECT A TUMOR. Proceed with utmost caution!");
    }
    final FittedPurity purity = context.bestFit();
    final FittedPurityScore purityScore = context.score();
    final List<PurpleCopyNumber> purpleCopyNumbers = PatientReporterHelper.loadPurpleCopyNumbers(runDirectory, sample);
    final List<GeneCopyNumber> panelGeneCopyNumbers = PatientReporterHelper.loadPurpleGeneCopyNumbers(runDirectory, sample).stream().filter(x -> reporterData().panelGeneModel().panel().contains(x.gene())).collect(Collectors.toList());
    LOGGER.info("  " + purpleCopyNumbers.size() + " purple copy number regions loaded for sample " + sample);
    LOGGER.info(" Analyzing purple somatic copy numbers...");
    final PurpleAnalysis purpleAnalysis = ImmutablePurpleAnalysis.builder().gender(context.gender()).status(context.status()).fittedPurity(purity).fittedScorePurity(purityScore).copyNumbers(purpleCopyNumbers).panelGeneCopyNumbers(panelGeneCopyNumbers).build();
    final Path structuralVariantVCF = PatientReporterHelper.findStructuralVariantVCF(runDirectory);
    LOGGER.info(" Loading structural variants...");
    final List<StructuralVariant> structuralVariants = StructuralVariantFileLoader.fromFile(structuralVariantVCF.toString(), true);
    LOGGER.info(" Enriching structural variants with purple data.");
    final List<EnrichedStructuralVariant> enrichedStructuralVariants = purpleAnalysis.enrichStructuralVariants(structuralVariants);
    LOGGER.info(" Analysing structural variants...");
    final StructuralVariantAnalysis structuralVariantAnalysis = structuralVariantAnalyzer().run(enrichedStructuralVariants, false);
    return ImmutableGenomeAnalysis.of(sample, variantAnalysis, purpleAnalysis, structuralVariantAnalysis);
}

Example 4 with PurityContext

use of com.hartwig.hmftools.common.purple.purity.PurityContext in project hmftools by hartwigmedical.

the class LoadStructuralVariants method enrichStructuralVariants.

@NotNull
private static List<EnrichedStructuralVariant> enrichStructuralVariants(@NotNull List<StructuralVariant> variants, @NotNull DatabaseAccess dbAccess, @NotNull String tumorSample) {
    final PurityContext purityContext = dbAccess.readPurityContext(tumorSample);
    if (purityContext == null) {
        LOGGER.warn("Unable to retrieve purple data. Enrichment may be incomplete.");
    }
    final PurityAdjuster purityAdjuster = purityContext == null ? new PurityAdjuster(Gender.FEMALE, 1, 1) : new PurityAdjuster(purityContext.gender(), purityContext.bestFit().purity(), purityContext.bestFit().normFactor());
    final List<PurpleCopyNumber> copyNumberList = dbAccess.readCopynumbers(tumorSample);
    final Multimap<String, PurpleCopyNumber> copyNumbers = Multimaps.index(copyNumberList, PurpleCopyNumber::chromosome);
    return EnrichedStructuralVariantFactory.enrich(variants, purityAdjuster, copyNumbers);
}