Examples with Haplotype org.dash.valid.gl.haplo.Haplotype used on opensource projects

Example 1 with Haplotype

use of org.dash.valid.gl.haplo.Haplotype in project ImmunogeneticDataTools by nmdp-bioinformatics.

the class HLALinkageDisequilibrium method findLinkedPairs.

private static Set<HaplotypePair> findLinkedPairs(LinkageDisequilibriumGenotypeList glString, EnumSet<Locus> loci, List<DisequilibriumElement> disequilibriumElements, DetectedLinkageFindings findings) {
    Set<HaplotypePair> linkedPairs = new HaplotypePairSet(new HaplotypePairComparator());
    Set<MultiLocusHaplotype> linkedHaplotypes = new HashSet<MultiLocusHaplotype>();
    Set<DetectedDisequilibriumElement> detectedDisequilibriumElements = new HashSet<DetectedDisequilibriumElement>();
    MultiLocusHaplotype clonedHaplotype = null;
    for (MultiLocusHaplotype possibleHaplotype : glString.getPossibleHaplotypes(loci)) {
        List<DisequilibriumElement> shortenedList = new ArrayList<DisequilibriumElement>(disequilibriumElements);
        HashMap<Locus, List<String>> hlaElementMap = new HashMap<Locus, List<String>>();
        for (Locus locus : possibleHaplotype.getLoci()) {
            if (loci.contains(locus)) {
                hlaElementMap.put(locus, possibleHaplotype.getAlleles(locus));
            }
        }
        DisequilibriumElement element = new CoreDisequilibriumElement(hlaElementMap, possibleHaplotype);
        DetectedDisequilibriumElement detectedElement = null;
        while (shortenedList.contains(element)) {
            int index = shortenedList.indexOf(element);
            clonedHaplotype = new MultiLocusHaplotype(new ConcurrentHashMap<Locus, List<String>>(possibleHaplotype.getAlleleMap()), possibleHaplotype.getHaplotypeInstanceMap(), possibleHaplotype.getDrb345Homozygous());
            detectedElement = new DetectedDisequilibriumElement(shortenedList.get(index));
            detectedElement.setHaplotype(element.getHaplotype());
            clonedHaplotype.setLinkage(detectedElement);
            linkedHaplotypes.add(clonedHaplotype);
            detectedDisequilibriumElements.add(detectedElement);
            shortenedList = shortenedList.subList(index + 1, shortenedList.size());
        }
    }
    findings.addLinkages(detectedDisequilibriumElements);
    for (Haplotype haplotype1 : linkedHaplotypes) {
        for (Haplotype haplotype2 : linkedHaplotypes) {
            int idx = 0;
            for (Locus locus : loci) {
                if ((!glString.hasHomozygous(locus) && haplotype1.getHaplotypeInstance(locus) == haplotype2.getHaplotypeInstance(locus))) {
                    // move on to next haplotype2
                    break;
                }
                if (idx == loci.size() - 1) {
                    linkedPairs.add(new HaplotypePair(haplotype1, haplotype2));
                }
                idx++;
            }
        }
    }
    return linkedPairs;
}

Example 2 with Haplotype

use of org.dash.valid.gl.haplo.Haplotype in project ImmunogeneticDataTools by nmdp-bioinformatics.

the class HLALinkageDisequilibrium method hasLinkageDisequilibrium.

public static Sample hasLinkageDisequilibrium(LinkageDisequilibriumGenotypeList glString, List<Haplotype> knownHaplotypes) {
    Set<HaplotypePair> linkedPairs = new HaplotypePairSet(new HaplotypePairComparator());
    Set<String> notCommon = GLStringUtilities.checkCommonWellDocumented(glString.getGLString());
    Set<String> notCIWD = GLStringUtilities.checkCommonIntermediateWellDocumented(glString.getGLString());
    Sample sample = new Sample(glString);
    DetectedLinkageFindings findings = new DetectedLinkageFindings(System.getProperty(Frequencies.FREQUENCIES_PROPERTY));
    Set<Linkages> linkages = LinkagesLoader.getInstance().getLinkages();
    if (linkages == null) {
        sample.setFindings(findings);
        return sample;
    }
    for (Linkages linkage : linkages) {
        EnumSet<Locus> loci = linkage.getLoci();
        findings.addFindingSought(loci);
        List<DisequilibriumElement> disequilibriumElements = HLAFrequenciesLoader.getInstance().getDisequilibriumElements(loci);
        List<Haplotype> enrichedHaplotypes = new ArrayList<Haplotype>();
        for (Haplotype haplotype : knownHaplotypes) {
            Haplotype enrichedHaplotype = enrichHaplotype(loci, disequilibriumElements, haplotype);
            if (enrichedHaplotype.getLinkage() != null) {
                findings.addLinkage(enrichedHaplotype.getLinkage());
                enrichedHaplotypes.add(enrichedHaplotype);
            }
        }
        if (enrichedHaplotypes.size() == 2) {
            linkedPairs.add(new HaplotypePair(enrichedHaplotypes.get(0), enrichedHaplotypes.get(1)));
        }
    }
    LOGGER.info(linkedPairs.size() + " linkedPairs");
    findings.setGenotypeList(glString);
    findings.setLinkedPairs(linkedPairs);
    findings.setNonCWDAlleles(notCommon);
    findings.setNonCIWDAlleles(notCIWD);
    findings.setHladb(System.getProperty(GLStringConstants.HLADB_PROPERTY));
    sample.setFindings(findings);
    return sample;
}

Example 3 with Haplotype

use of org.dash.valid.gl.haplo.Haplotype in project ImmunogeneticDataTools by nmdp-bioinformatics.

the class LinkageDisequilibriumGenotypeListTest method testHaplotypePairs.

@Test
public void testHaplotypePairs() throws IOException {
    LinkageDisequilibriumGenotypeList genotypeList = new LinkageDisequilibriumGenotypeList("HaplotypePairs", TEST_BC_PAIRS);
    Set<Locus> loci = new HashSet<Locus>();
    loci.add(Locus.HLA_B);
    loci.add(Locus.HLA_C);
    Set<MultiLocusHaplotype> possibleHaplotypes = genotypeList.constructPossibleHaplotypes(loci);
    Set<HaplotypePair> linkedPairs = new HaplotypePairSet(new HaplotypePairComparator());
    for (Haplotype haplotype1 : possibleHaplotypes) {
        for (Haplotype haplotype2 : possibleHaplotypes) {
            if ((!genotypeList.hasHomozygous(Locus.HLA_B) && haplotype1.getAlleles(Locus.HLA_B).containsAll(haplotype2.getAlleles(Locus.HLA_B))) || (!genotypeList.hasHomozygous(Locus.HLA_C) && haplotype1.getAlleles(Locus.HLA_C).containsAll(haplotype2.getAlleles(Locus.HLA_C)))) {
                continue;
            }
            HaplotypePair haplotypePair = new HaplotypePair(haplotype1, haplotype2);
            linkedPairs.add(haplotypePair);
        }
    }
    for (HaplotypePair pair : linkedPairs) {
        Haplotype haplotype1 = pair.getHaplotypes().get(0);
        assertTrue(haplotype1 instanceof MultiLocusHaplotype);
        Haplotype haplotype2 = pair.getHaplotypes().get(1);
        assertTrue(haplotype2 instanceof MultiLocusHaplotype);
        assertTrue((haplotype1.getAlleles(Locus.HLA_B).contains(B0704) && haplotype2.getAlleles(Locus.HLA_B).contains(B4403)) || (haplotype1.getAlleles(Locus.HLA_B).contains(B4403) && haplotype2.getAlleles(Locus.HLA_B).contains(B0704)));
        assertTrue((haplotype1.getAlleles(Locus.HLA_C).contains(C0702) && haplotype2.getAlleles(Locus.HLA_C).contains(C1203)) || (haplotype1.getAlleles(Locus.HLA_C).contains(C1203) && haplotype2.getAlleles(Locus.HLA_C).contains(C0702)));
        assertFalse(haplotype1.getAlleles(Locus.HLA_B).contains(B0704) && haplotype2.getAlleles(Locus.HLA_B).contains(B0704));
        assertFalse(haplotype1.getAlleles(Locus.HLA_B).contains(B4403) && haplotype2.getAlleles(Locus.HLA_B).contains(B4403));
        assertFalse(haplotype1.getAlleles(Locus.HLA_C).contains(C0702) && haplotype2.getAlleles(Locus.HLA_C).contains(C0702));
        assertFalse(haplotype1.getAlleles(Locus.HLA_C).contains(C1203) && haplotype2.getAlleles(Locus.HLA_C).contains(C1203));
    }
}

Example 4 with Haplotype

use of org.dash.valid.gl.haplo.Haplotype in project ImmunogeneticDataTools by nmdp-bioinformatics.

the class LinkageDisequilibriumAnalyzerTest method testPhasedGenotypeList.

@Test
public void testPhasedGenotypeList() throws IOException {
    System.setProperty(Frequencies.FREQUENCIES_PROPERTY, Frequencies.NMDP.getShortName());
    String fullyQualified = GLStringUtilities.fullyQualifyGLString("HLA-A*24:02:01:01~HLA-C*04:01:01:06~HLA-B*35:02:01~HLA-DRB3*02:02:01:02~HLA-DRB1*11:01:01:01~HLA-DQA1*05:05:01:01/HLA-DQA1*05:05:01:02~HLA-DQB1*03:01:01:03~HLA-DPA1*01:03:01:01~HLA-DPB1*05:01:01+HLA-A*11:01:01:01~HLA-C*12:03:01:01~HLA-B*35:03:01~HLA-DRB3*02:02:01:01~HLA-DRB1*13:01:01:01/HLA-DRB1*13:01:01:02~HLA-DQA1*01:03:01:02~HLA-DQB1*06:03:01~HLA-DPA1*02:01:01:01~HLA-DPB1*13:01:01/HLA-DPB1*107:01");
    LinkageDisequilibriumGenotypeList glString = new LinkageDisequilibriumGenotypeList("SBCFMW0003", fullyQualified);
    List<Haplotype> knownHaplotypes = GLStringUtilities.buildHaplotypes(glString);
    Sample sample = HLALinkageDisequilibrium.hasLinkageDisequilibrium(glString, knownHaplotypes);
    assertNotNull(sample);
}

Example 5 with Haplotype

use of org.dash.valid.gl.haplo.Haplotype in project ImmunogeneticDataTools by nmdp-bioinformatics.

the class GLStringUtilities method buildHaplotypes.

public static List<Haplotype> buildHaplotypes(LinkageDisequilibriumGenotypeList linkedGlString) {
    String glString = linkedGlString.getGLString();
    List<Haplotype> knownHaplotypes = new CopyOnWriteArrayList<Haplotype>();
    HashMap<String, Locus> locusMap = new HashMap<String, Locus>();
    Locus locus = null;
    if (StringUtils.countMatches(glString, GLStringConstants.GENE_PHASE_DELIMITER) > 1 && StringUtils.countMatches(glString, GLStringConstants.GENE_COPY_DELIMITER) == 1) {
        List<String> genes = GLStringUtilities.parse(glString, GLStringConstants.GENE_DELIMITER);
        for (String gene : genes) {
            List<String> genotypeAmbiguities = GLStringUtilities.parse(gene, GLStringConstants.GENOTYPE_AMBIGUITY_DELIMITER);
            for (String genotypeAmbiguity : genotypeAmbiguities) {
                List<String> geneCopies = GLStringUtilities.parse(genotypeAmbiguity, GLStringConstants.GENE_COPY_DELIMITER);
                int i = 0;
                for (String geneCopy : geneCopies) {
                    HashMap<Locus, SingleLocusHaplotype> singleLocusHaplotypes = new HashMap<Locus, SingleLocusHaplotype>();
                    List<String> genePhases = GLStringUtilities.parse(geneCopy, GLStringConstants.GENE_PHASE_DELIMITER);
                    for (String genePhase : genePhases) {
                        String[] splitString = genePhase.split(GLStringUtilities.ESCAPED_ASTERISK);
                        String locusVal = splitString[0];
                        List<String> alleleAmbiguities = GLStringUtilities.parse(genePhase, GLStringConstants.ALLELE_AMBIGUITY_DELIMITER);
                        if (locusMap.containsKey(locusVal)) {
                            locus = locusMap.get(locusVal);
                        } else {
                            locus = Locus.normalizeLocus(Locus.lookup(locusVal));
                            locusMap.put(locusVal, locus);
                        }
                        SingleLocusHaplotype haplotype = new SingleLocusHaplotype(locus, alleleAmbiguities, i);
                        singleLocusHaplotypes.put(locus, haplotype);
                    }
                    MultiLocusHaplotype multiLocusHaplotype = new MultiLocusHaplotype(singleLocusHaplotypes, linkedGlString.hasHomozygous(Locus.HLA_DRB345));
                    multiLocusHaplotype.setSequence(i + 1);
                    knownHaplotypes.add(multiLocusHaplotype);
                    i++;
                }
            }
        }
    }
    return knownHaplotypes;
}