use of dr.app.util.Arguments.ArgumentException in project beast-mcmc by beast-dev.
the class BeagleSequenceSimulatorConsoleApp method simulate.
// END: constructor
public void simulate(String[] args) {
try {
// /////////////////////////////////
// ---SPLIT PARTITION ARGUMENTS---//
// /////////////////////////////////
int from = 0;
int to = 0;
ArrayList<String[]> argsList = new ArrayList<String[]>();
for (String arg : args) {
if (arg.equalsIgnoreCase(SPLIT_PARTITION)) {
argsList.add(Arrays.copyOfRange(args, from, to));
from = to + 1;
}
// END: split check
to++;
}
if (args[0].contains(HELP)) {
gracefullyExit(null);
} else if (argsList.size() == 0) {
gracefullyExit("Empty or incorrect arguments list.");
}
// END: failed split check
String[] leftoverArguments = Arrays.copyOfRange(args, from, args.length);
if (leftoverArguments.length > 2) {
gracefullyExit("Unrecognized option " + leftoverArguments[2]);
}
ArrayList<Partition> partitionsList = new ArrayList<Partition>();
for (String[] partitionArgs : argsList) {
// /////////////
// ---PARSE---//
// /////////////
arguments.parseArguments(partitionArgs);
// ///////////////////
// ---INTERROGATE---//
// ///////////////////
PartitionData data = new PartitionData();
String option = null;
double[] values = null;
if (partitionArgs.length == 0 || arguments.hasOption(HELP)) {
gracefullyExit(null);
}
// Tree / Taxa
if (arguments.hasOption(TREE_FILE)) {
File treeFile = new File(arguments.getStringOption(TREE_FILE));
Tree tree = Utils.importTreeFromFile(treeFile);
data.record = new TreesTableRecord(treeFile.getName(), tree);
} else if (arguments.hasOption(TAXA_SET)) {
File taxaFile = new File(arguments.getStringOption(TAXA_SET));
Taxa taxa = Utils.importTaxaFromFile(taxaFile);
data.record = new TreesTableRecord(taxaFile.getName(), taxa);
} else {
throw new RuntimeException("Tree file / Taxa set not specified.");
}
// Demographic Model
if (arguments.hasOption(DEMOGRAPHIC_MODEL)) {
option = arguments.getStringOption(DEMOGRAPHIC_MODEL);
if (option.equalsIgnoreCase(NO_DEMOGRAPHIC_MODEL)) {
int index = 0;
data.demographicModelIndex = index;
} else if (option.equalsIgnoreCase(CONSTANT_POPULATION)) {
int index = 1;
data.demographicModelIndex = index;
if (arguments.hasOption(CONSTANT_POPULATION_PARAMETER_VALUES)) {
values = arguments.getRealArrayOption(CONSTANT_POPULATION_PARAMETER_VALUES);
parseDemographicValues(index, values, data);
}
} else if (option.equalsIgnoreCase(EXPONENTIAL_GROWTH_RATE)) {
int index = 2;
data.demographicModelIndex = index;
if (arguments.hasOption(EXPONENTIAL_GROWTH_RATE_PARAMETER_VALUES)) {
values = arguments.getRealArrayOption(EXPONENTIAL_GROWTH_RATE_PARAMETER_VALUES);
parseDemographicValues(index, values, data);
}
} else if (option.equalsIgnoreCase(EXPONENTIAL_DOUBLING_TIME)) {
int index = 3;
data.demographicModelIndex = index;
if (arguments.hasOption(EXPONENTIAL_GROWTH_DOUBLING_TIME_PARAMETER_VALUES)) {
values = arguments.getRealArrayOption(EXPONENTIAL_GROWTH_DOUBLING_TIME_PARAMETER_VALUES);
parseDemographicValues(index, values, data);
}
} else {
gracefullyExit("Unrecognized option.");
}
}
// Branch Substitution Model
if (arguments.hasOption(BRANCH_SUBSTITUTION_MODEL)) {
option = arguments.getStringOption(BRANCH_SUBSTITUTION_MODEL);
if (option.equalsIgnoreCase(HKY)) {
int index = 0;
data.substitutionModelIndex = index;
if (arguments.hasOption(HKY_SUBSTITUTION_PARAMETER_VALUES)) {
values = arguments.getRealArrayOption(HKY_SUBSTITUTION_PARAMETER_VALUES);
parseSubstitutionValues(index, values, data);
}
} else if (option.equalsIgnoreCase(GTR)) {
int index = 1;
data.substitutionModelIndex = index;
if (arguments.hasOption(GTR_SUBSTITUTION_PARAMETER_VALUES)) {
values = arguments.getRealArrayOption(GTR_SUBSTITUTION_PARAMETER_VALUES);
parseSubstitutionValues(index, values, data);
}
} else if (option.equalsIgnoreCase(TN93)) {
int index = 2;
data.substitutionModelIndex = index;
if (arguments.hasOption(TN93_SUBSTITUTION_PARAMETER_VALUES)) {
values = arguments.getRealArrayOption(TN93_SUBSTITUTION_PARAMETER_VALUES);
parseSubstitutionValues(index, values, data);
}
} else if (option.equalsIgnoreCase(GY94_CODON_MODEL)) {
int index = 3;
data.substitutionModelIndex = index;
if (arguments.hasOption(GY94_SUBSTITUTION_PARAMETER_VALUES)) {
values = arguments.getRealArrayOption(GY94_SUBSTITUTION_PARAMETER_VALUES);
parseSubstitutionValues(index, values, data);
}
} else {
gracefullyExit("Unrecognized option.");
}
}
// Site Rate Model
if (arguments.hasOption(SITE_RATE_MODEL)) {
option = arguments.getStringOption(SITE_RATE_MODEL);
if (option.equalsIgnoreCase(NO_SITE_RATE_MODEL)) {
int index = 0;
data.siteRateModelIndex = index;
} else if (option.equalsIgnoreCase(GAMMA_SITE_RATE_MODEL)) {
int index = 1;
data.siteRateModelIndex = index;
if (arguments.hasOption(GAMMA_SITE_RATE_MODEL_PARAMETER_VALUES)) {
values = arguments.getRealArrayOption(GAMMA_SITE_RATE_MODEL_PARAMETER_VALUES);
parseSiteRateValues(index, values, data);
}
} else {
gracefullyExit("Unrecognized option.");
}
}
// Clock Rate Model
if (arguments.hasOption(CLOCK_RATE_MODEL)) {
option = arguments.getStringOption(CLOCK_RATE_MODEL);
if (option.equalsIgnoreCase(STRICT_CLOCK)) {
int index = 0;
data.clockModelIndex = index;
if (arguments.hasOption(STRICT_CLOCK_PARAMETER_VALUES)) {
values = arguments.getRealArrayOption(STRICT_CLOCK_PARAMETER_VALUES);
parseClockValues(index, values, data);
}
} else if (option.equalsIgnoreCase(LOGNORMAL_RELAXED_CLOCK)) {
int index = 1;
data.clockModelIndex = index;
if (arguments.hasOption(LOGNORMAL_RELAXED_CLOCK_PARAMETER_VALUES)) {
values = arguments.getRealArrayOption(LOGNORMAL_RELAXED_CLOCK_PARAMETER_VALUES);
parseClockValues(index, values, data);
}
// set to true/false
if (arguments.hasOption(LRC_PARAMETERS_IN_REAL_SPACE)) {
boolean lrcParametersInRealSpace = (arguments.getStringOption(LRC_PARAMETERS_IN_REAL_SPACE).equalsIgnoreCase(TRUE) ? true : false);
data.lrcParametersInRealSpace = lrcParametersInRealSpace;
}
} else if (option.equalsIgnoreCase(EXPONENTIAL_RELAXED_CLOCK)) {
int index = 2;
data.clockModelIndex = index;
if (arguments.hasOption(EXPONENTIAL_RELAXED_CLOCK_PARAMETER_VALUES)) {
values = arguments.getRealArrayOption(EXPONENTIAL_RELAXED_CLOCK_PARAMETER_VALUES);
parseClockValues(index, values, data);
}
} else if (option.equalsIgnoreCase(INVERSE_GAUSSIAN_RELAXED_CLOCK)) {
int index = 3;
data.clockModelIndex = index;
if (arguments.hasOption(INVERSE_GAUSSIAN_RELAXED_CLOCK_PARAMETER_VALUES)) {
values = arguments.getRealArrayOption(INVERSE_GAUSSIAN_RELAXED_CLOCK_PARAMETER_VALUES);
parseClockValues(index, values, data);
}
} else {
gracefullyExit("Unrecognized option.");
}
}
// Frequency Model
if (arguments.hasOption(BASE_FREQUENCIES)) {
option = arguments.getStringOption(BASE_FREQUENCIES);
if (option.equalsIgnoreCase(NUCLEOTIDE_FREQUENCIES)) {
int index = 0;
data.frequencyModelIndex = index;
if (arguments.hasOption(NUCLEOTIDE_FREQUENCY_PARAMETER_VALUES)) {
values = arguments.getRealArrayOption(NUCLEOTIDE_FREQUENCY_PARAMETER_VALUES);
parseFrequencyValues(index, values, data);
}
} else if (option.equalsIgnoreCase(CODON_FREQUENCIES)) {
int index = 1;
data.frequencyModelIndex = index;
if (arguments.hasOption(CODON_FREQUENCY_PARAMETER_VALUES)) {
values = arguments.getRealArrayOption(CODON_FREQUENCY_PARAMETER_VALUES);
parseFrequencyValues(index, values, data);
}
} else {
gracefullyExit("Unrecognized option.");
}
}
if (arguments.hasOption(FROM)) {
data.from = arguments.getIntegerOption(FROM);
}
if (arguments.hasOption(TO)) {
data.to = arguments.getIntegerOption(TO);
}
if (arguments.hasOption(EVERY)) {
data.every = arguments.getIntegerOption(EVERY);
}
// END: EVERY option check
// create partition
Partition partition = new Partition(//
data.createTreeModel(), //
data.createBranchModel(), //
data.createSiteRateModel(), //
data.createClockRateModel(), //
data.createFrequencyModel(), // from
data.from - 1, // to
data.to - 1, // every
data.every);
if (arguments.hasOption(ROOT_SEQUENCE)) {
data.ancestralSequenceString = arguments.getStringOption(ROOT_SEQUENCE);
partition.setRootSequence(data.createAncestralSequence());
}
// END: ANCESTRAL_SEQUENCE option check
partitionsList.add(partition);
// System.err.println(data.from);
dataList.add(data);
}
if (this.VERBOSE) {
// System.out.println(dataList.get(0).from + " " + dataList.get(1).from);
Utils.printPartitionDataList(dataList);
System.out.println();
}
SimpleAlignment alignment = new SimpleAlignment();
String outputFile = null;
if (leftoverArguments.length > 0) {
outputFile = leftoverArguments[0];
String[] file = outputFile.split("\\.", 2);
if (file.length > 1) {
String extension = outputFile.split("\\.", 2)[1];
// TODO Delegate here to enum-class; switches are not generic
if (extension.equalsIgnoreCase(SimpleAlignment.OutputType.FASTA.getText()) || extension.equalsIgnoreCase("fst")) {
dataList.outputFormat = SimpleAlignment.OutputType.FASTA;
} else if (extension.equalsIgnoreCase(SimpleAlignment.OutputType.NEXUS.getText()) || extension.equalsIgnoreCase("nxs")) {
dataList.outputFormat = SimpleAlignment.OutputType.NEXUS;
} else if (extension.equalsIgnoreCase(SimpleAlignment.OutputType.XML.getText())) {
dataList.outputFormat = SimpleAlignment.OutputType.XML;
} else {
dataList.outputFormat = SimpleAlignment.OutputType.FASTA;
}
//END: extension check
} else {
outputFile = file[0] + "." + SimpleAlignment.OutputType.FASTA.toString().toLowerCase();
dataList.outputFormat = SimpleAlignment.OutputType.FASTA;
}
//END:
}
if (leftoverArguments.length > 1) {
dataList.startingSeed = Long.parseLong(leftoverArguments[1]);
dataList.setSeed = true;
}
if (dataList.setSeed) {
MathUtils.setSeed(dataList.startingSeed);
}
if (leftoverArguments.length > 2) {
dataList.outputAncestralSequences = Boolean.parseBoolean(leftoverArguments[2]);
}
if (leftoverArguments.length > 3) {
dataList.useParallel = Boolean.parseBoolean(leftoverArguments[3]);
}
BeagleSequenceSimulator beagleSequenceSimulator = new BeagleSequenceSimulator(partitionsList);
alignment = beagleSequenceSimulator.simulate(dataList.useParallel, dataList.outputAncestralSequences);
alignment.setOutputType(dataList.outputFormat);
PrintWriter writer = new PrintWriter(new FileWriter(outputFile));
writer.println(alignment.toString());
writer.close();
} catch (ArgumentException e) {
System.out.println();
printUsage(arguments);
System.out.println();
System.out.println(e.getMessage());
e.printStackTrace();
System.exit(1);
} catch (IOException e) {
System.out.println();
printUsage(arguments);
System.out.println();
System.out.println(e.getMessage());
e.printStackTrace();
System.exit(1);
} catch (ImportException e) {
System.out.println();
printUsage(arguments);
System.out.println();
System.out.println(e.getMessage());
e.printStackTrace();
System.exit(1);
}
// END: try-catch block
}
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