Examples with ConversionGraph bacter.ConversionGraph used on opensource projects

Example 6 with ConversionGraph

use of bacter.ConversionGraph in project bacter by tgvaughan.

the class ACGLikelihoodTest method testLikelihoodUsingSimulatedData.

@Test
public void testLikelihoodUsingSimulatedData() throws Exception {
    ConstantPopulation popFunc = new ConstantPopulation();
    popFunc.initByName("popSize", new RealParameter("1.0"));
    Locus locus = new Locus("locus", 10000);
    TaxonSet taxonSet = getTaxonSet(10);
    ConversionGraph acg = new SimulatedACG();
    acg.initByName("rho", 5.0 / locus.getSiteCount(), "delta", 1000.0, "populationModel", popFunc, "locus", locus, "taxonset", taxonSet);
    System.out.println(acg);
    // Site model:
    JukesCantor jc = new JukesCantor();
    jc.initByName();
    SiteModel siteModel = new SiteModel();
    siteModel.initByName("mutationRate", new RealParameter("1"), "substModel", jc);
    // Simulate alignment:
    SimulatedAlignment alignment = new SimulatedAlignment();
    alignment.initByName("acg", acg, "siteModel", siteModel, "outputFileName", "simulated_alignment.nexus", "useNexus", true);
    // Calculate likelihood:
    ACGLikelihood argLikelihood = new ACGLikelihood();
    argLikelihood.initByName("locus", locus, "data", alignment, "tree", acg, "siteModel", siteModel);
    double logP = argLikelihood.calculateLogP();
    // Compare product of likelihoods of "marginal alignments" with
    // likelihood computed using RGL.
    ACGLikelihoodSlow argLikelihoodSlow = new ACGLikelihoodSlow();
    argLikelihoodSlow.initByName("locus", locus, "data", alignment, "tree", acg, "siteModel", siteModel);
    double logPprime = argLikelihoodSlow.calculateLogP();
    double relError = 2.0 * Math.abs(logP - logPprime) / Math.abs(logP + logPprime);
    System.out.format("logP=%g\nlogPprime=%g\nrelError=%g\n", logP, logPprime, relError);
    assertTrue(relError < 1e-13);
}

Example 7 with ConversionGraph

use of bacter.ConversionGraph in project bacter by tgvaughan.

the class ACGLikelihoodTest method testBeagleLikelihood.

@Test
public void testBeagleLikelihood() throws Exception {
    Locus locus = new Locus("locus", getAlignment());
    // ConversionGraph
    ConversionGraph acg = new ConversionGraph();
    ClusterTree tree = new ClusterTree();
    tree.initByName("clusterType", "upgma", "taxa", locus.getAlignment());
    acg.assignFrom(tree);
    acg.initByName("locus", locus);
    // Site model:
    JukesCantor jc = new JukesCantor();
    jc.initByName();
    SiteModel siteModel = new SiteModel();
    siteModel.initByName("substModel", jc);
    // Likelihood
    ACGLikelihoodBeagle argLikelihood = new ACGLikelihoodBeagle();
    argLikelihood.initByName("locus", locus, "tree", acg, "siteModel", siteModel);
    ACGLikelihoodSlow argLikelihoodSlow = new ACGLikelihoodSlow();
    argLikelihoodSlow.initByName("locus", locus, "tree", acg, "siteModel", siteModel);
    acg.setEverythingDirty(true);
    try {
        double logP = argLikelihood.calculateLogP();
        double logPtrue = argLikelihoodSlow.calculateLogP();
        double relativeDiff = Math.abs(2.0 * (logPtrue - logP) / (logPtrue + logP));
        assertTrue(relativeDiff < 1e-14);
        // Add a single recombination event
        Node node1 = acg.getExternalNodes().get(0);
        Node node2 = node1.getParent();
        double height1 = 0.5 * (node1.getHeight() + node1.getParent().getHeight());
        double height2 = 0.5 * (node2.getHeight() + node2.getParent().getHeight());
        int startLocus = 100;
        int endLocus = 200;
        Conversion recomb1 = new Conversion(node1, height1, node2, height2, startLocus, endLocus, acg, locus);
        acg.addConversion(recomb1);
        logP = argLikelihood.calculateLogP();
        logPtrue = argLikelihoodSlow.calculateLogP();
        relativeDiff = Math.abs(2.0 * (logPtrue - logP) / (logPtrue + logP));
        assertTrue(relativeDiff < 1e-14);
        // Add another recombination event
        node1 = acg.getExternalNodes().get(0);
        node2 = acg.getNode(20);
        height1 = 0.75 * (node1.getHeight() + node1.getParent().getHeight());
        height2 = 0.5 * (node2.getHeight() + node2.getParent().getHeight());
        startLocus = 250;
        endLocus = 300;
        Conversion recomb2 = new Conversion(node1, height1, node2, height2, startLocus, endLocus, acg, locus);
        acg.addConversion(recomb2);
        logP = argLikelihood.calculateLogP();
        logPtrue = argLikelihoodSlow.calculateLogP();
        relativeDiff = Math.abs(2.0 * (logPtrue - logP) / (logPtrue + logP));
        assertTrue(relativeDiff < 1e-14);
    } catch (RuntimeException ex) {
        System.err.println("Beagle library not found: skipping beagle likelihood test.");
    }
}

Example 8 with ConversionGraph

use of bacter.ConversionGraph in project bacter by tgvaughan.

the class ACGLikelihoodTest method testLikelihoodFixedData.

@Test
public void testLikelihoodFixedData() throws Exception {
    Locus locus = new Locus("locus", getAlignment());
    // ConversionGraph
    ConversionGraph acg = new ConversionGraph();
    ClusterTree tree = new ClusterTree();
    tree.initByName("clusterType", "upgma", "taxa", locus.getAlignment());
    acg.assignFrom(tree);
    acg.initByName("locus", locus);
    // Site model:
    JukesCantor jc = new JukesCantor();
    jc.initByName();
    SiteModel siteModel = new SiteModel();
    siteModel.initByName("substModel", jc);
    // Likelihood
    ACGLikelihood argLikelihood = new ACGLikelihood();
    argLikelihood.initByName("locus", locus, "tree", acg, "siteModel", siteModel);
    ACGLikelihoodSlow argLikelihoodSlow = new ACGLikelihoodSlow();
    argLikelihoodSlow.initByName("locus", locus, "tree", acg, "siteModel", siteModel);
    acg.setEverythingDirty(true);
    double logP = argLikelihood.calculateLogP();
    double logPtrue = argLikelihoodSlow.calculateLogP();
    double relativeDiff = Math.abs(2.0 * (logPtrue - logP) / (logPtrue + logP));
    assertTrue(relativeDiff < 1e-14);
    // Add a single recombination event
    Node node1 = acg.getExternalNodes().get(0);
    Node node2 = node1.getParent();
    double height1 = 0.5 * (node1.getHeight() + node1.getParent().getHeight());
    double height2 = 0.5 * (node2.getHeight() + node2.getParent().getHeight());
    int startLocus = 100;
    int endLocus = 200;
    Conversion recomb1 = new Conversion(node1, height1, node2, height2, startLocus, endLocus, acg, locus);
    acg.addConversion(recomb1);
    logP = argLikelihood.calculateLogP();
    logPtrue = argLikelihoodSlow.calculateLogP();
    relativeDiff = Math.abs(2.0 * (logPtrue - logP) / (logPtrue + logP));
    assertTrue(relativeDiff < 1e-14);
    // Add another recombination event
    node1 = acg.getExternalNodes().get(0);
    node2 = acg.getNode(20);
    height1 = 0.75 * (node1.getHeight() + node1.getParent().getHeight());
    height2 = 0.5 * (node2.getHeight() + node2.getParent().getHeight());
    startLocus = 250;
    endLocus = 300;
    Conversion recomb2 = new Conversion(node1, height1, node2, height2, startLocus, endLocus, acg, locus);
    acg.addConversion(recomb2);
    logP = argLikelihood.calculateLogP();
    logPtrue = argLikelihoodSlow.calculateLogP();
    relativeDiff = Math.abs(2.0 * (logPtrue - logP) / (logPtrue + logP));
    assertTrue(relativeDiff < 1e-14);
}

Example 9 with ConversionGraph

use of bacter.ConversionGraph in project bacter by tgvaughan.

the class DifferenceFromTrueACG method main.

public static void main(String[] args) throws IOException, XMLStreamException {
    Options options = processArguments(args);
    // Load true ARG
    BacterACGLogReader truthReader = new BacterACGLogReader(options.truthFile, 0);
    if (truthReader.getACGCount() != 1) {
        System.out.println("Expected exactly 1 ACG in truth file. Found " + truthReader.getACGCount());
        System.exit(1);
    }
    ConversionGraph trueACG = null;
    for (ConversionGraph acg : truthReader) trueACG = acg;
    // Determine clades present in truth
    Clade[] trueClades = new Clade[trueACG.getNodeCount()];
    getClades(trueClades, trueACG.getRoot());
    Set<Clade> trueCladeSet = new HashSet<>(Arrays.asList(trueClades));
    // Set up histograms
    Map<Clade, Integer> cladeHist = new HashMap<>();
    for (Clade clade : trueClades) cladeHist.put(clade, 0);
    Map<Conversion, Integer> convHist = new HashMap<>();
    for (Conversion conv : trueACG.getConversions(trueACG.getLoci().get(0))) convHist.put(conv, 0);
    // Set up ARG log file reader
    ACGLogReader logReader;
    if (options.useCOFormat) {
        logReader = new COACGLogFileReader(options.logFile, options.burninPerc);
    } else {
        logReader = new BacterACGLogReader(options.logFile, options.burninPerc);
    }
    try (PrintStream ps = new PrintStream(options.outFile)) {
        ps.println("trueCladeCount sampledTrueCladeCount trueConvCount sampledConvCount sampledTrueConvCount");
        for (ConversionGraph acg : logReader) {
            Clade[] clades = new Clade[acg.getNodeCount()];
            getClades(clades, acg.getRoot());
            List<Double> timeErrors = new ArrayList<>();
            int sampledTrueClades = countSampledTrueClades(trueClades, clades, options.ageTol, cladeHist);
            int sampledTrueConvs = countSampledTrueConversions(trueACG, trueClades, acg, clades, options.boundaryTol, options.ageTol, convHist);
            ps.println(trueACG.getNodeCount() + "\t" + sampledTrueClades + "\t" + trueACG.getConvCount(trueACG.getLoci().get(0)) + "\t" + acg.getConvCount(acg.getLoci().get(0)) + "\t" + sampledTrueConvs);
        }
    }
    try (PrintStream ps = new PrintStream(options.summaryFile)) {
        ps.println("trueCladeCount recoveredCladeCount trueConvCount recoveredConvCount");
        int recoveredTrueClades = countRecoveredTrueClades(cladeHist, logReader.getCorrectedACGCount(), 0.5);
        int recoveredTrueConvs = countRecoveredTrueConvs(convHist, logReader.getCorrectedACGCount(), 0.5);
        ps.println(trueACG.getNodeCount() + "\t" + recoveredTrueClades + "\t" + trueACG.getConvCount(trueACG.getLoci().get(0)) + "\t" + recoveredTrueConvs);
    }
}

Example 10 with ConversionGraph

use of bacter.ConversionGraph in project bacter by tgvaughan.

the class PiecewisePopulationFunction method main.

/**
 * Main method for testing.
 *
 * @param args command line arguments (unused)
 */
public static void main(String[] args) throws Exception {
    String acgString = "[&15,0,1.3905355989030808,31,770,1.597708055397074] " + "[&30,931,2.4351280458424904,36,2486,3.78055549386568] " + "[&15,941,2.0439957300083322,38,2364,6.911056700367016] " + "[&36,1091,4.285505683622974,38,2589,9.867725913197855] " + "((((10:0.5385300170206817,(17:0.116794353049212," + "((3:0.039229346597297564,12:0.039229346597297564)23:0.04582913870888949," + "13:0.08505848530618705)24:0.03173586774302495)26:0.4217356639714697)28:1.8114199763246093," + "((8:0.10883006062265468,2:0.10883006062265468)25:0.556428062025291," + "(6:0.5393311342677402,11:0.5393311342677402)29:0.12592698838020555)31:1.6846918706973453)34:1.4536824928125807," + "(1:0.47184545557390367,14:0.47184545557390367)27:3.331787030583968)37:2.9704369411362554," + "(((15:2.0624287390593707,((16:0.01825347077733299,19:0.01825347077733299)21:0.7668749128372041," + "(7:0.008018731329538273,9:0.008018731329538273)20:0.7771096522849988)32:1.2773003554448337)33:0.7487092404613747," + "4:2.8111379795207454)35:0.1331794525400949,((0:0.0243537216663141," + "5:0.0243537216663141)22:0.5681537100482162,18:0.5925074317145304)30:2.35181000034631)36:3.829751995233287)38:0.0";
    ConversionGraph acg = new ConversionGraph();
    acg.initByName("siteCount", 10000, "fromString", acgString);
    PiecewisePopulationFunction skyline = new PiecewisePopulationFunction();
    skyline.initByName("acg", acg, "popSizes", new RealParameter("1.0 1.0 5.0 1.0 2.0"), "groupSizes", new IntegerParameter("0"), "piecewiseLinear", true);
    try (PrintStream ps = new PrintStream("out.txt")) {
        ps.println("t N intensity intensityInv");
        double t = 0.0;
        while (t < 10) {
            ps.format("%g %g %g %g\n", t, skyline.getPopSize(t), skyline.getIntensity(t), skyline.getInverseIntensity(skyline.getIntensity(t)));
            t += 0.001;
        }
        ps.close();
    }
}