org.jax.bioinfdata.genocall.ConvertAlchemyCallsToHDF5Main.java Source code

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Here is the source code for org.jax.bioinfdata.genocall.ConvertAlchemyCallsToHDF5Main.java

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/*
 * Copyright (c) 2010 The Jackson Laboratory
 * 
 * This is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * This software is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this software.  If not, see <http://www.gnu.org/licenses/>.
 */

package org.jax.bioinfdata.genocall;

import java.io.File;
import java.io.FileReader;
import java.io.IOException;

import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.CommandLineParser;
import org.apache.commons.cli.GnuParser;
import org.apache.commons.cli.HelpFormatter;
import org.apache.commons.cli.Option;
import org.apache.commons.cli.Options;
import org.apache.commons.cli.ParseException;
import org.jax.util.io.CommonFlatFileFormat;
import org.jax.util.io.FlatFileReader;
import org.jax.util.io.IllegalFormatException;

import ch.systemsx.cisd.hdf5.HDF5FactoryProvider;
import ch.systemsx.cisd.hdf5.IHDF5Factory;
import ch.systemsx.cisd.hdf5.IHDF5Writer;

/**
 * @author <A HREF="mailto:keith.sheppard@jax.org">Keith Sheppard</A>
 */
public class ConvertAlchemyCallsToHDF5Main {
    /**
     * the main entry point
     * @param args  command line args
     * @throws IOException
     * @throws IllegalFormatException
     */
    public static void main(String[] args) throws IllegalFormatException, IOException {
        // Deal with the options.
        CommandLineParser parser = new GnuParser();
        Options options = new Options();
        CommandLine commandLine = null;

        final Option helpOption;
        {
            helpOption = new Option("help", "Print this help and exit");
            helpOption.setRequired(false);
            options.addOption(helpOption);
        }

        final Option genoFileOption;
        {
            genoFileOption = new Option("alchemygenos", "the genotype calls output from alchemy");
            genoFileOption.setRequired(true);
            genoFileOption.setArgs(1);
            genoFileOption.setArgName("file name");
            options.addOption(genoFileOption);
        }

        final Option outputFileOption;
        {
            outputFileOption = new Option("hdf5out", "the file to write HDF5 output to");
            outputFileOption.setRequired(true);
            outputFileOption.setArgs(1);
            outputFileOption.setArgName("file name");
            options.addOption(outputFileOption);
        }

        try {
            commandLine = parser.parse(options, args);

            // See if we just need to print the help options.
            if (commandLine.hasOption(helpOption.getOpt())) {
                HelpFormatter helpFormatter = new HelpFormatter();
                helpFormatter.printHelp("alchtohdf5", options);
            } else {
                final String genoFileName = commandLine.getOptionValue(genoFileOption.getOpt());
                final String outFileName = commandLine.getOptionValue(outputFileOption.getOpt());

                final FlatFileReader genoFFR = new FlatFileReader(new FileReader(genoFileName),
                        CommonFlatFileFormat.TAB_DELIMITED_UNIX);

                GenotypeCallMatrix genoMat = GenotypesFlatFile.readAlchemyGenoCalls(genoFFR);
                genoFFR.close();

                IHDF5Factory hdf5Fac = HDF5FactoryProvider.get();
                File hdf5File = new File(outFileName);
                if (hdf5File.exists()) {
                    if (!hdf5File.delete()) {
                        throw new IOException("failed to overwrite \"" + outFileName + "\"");
                    }
                }
                IHDF5Writer hdf5Writer = hdf5Fac.open(hdf5File);
                HDF5GenotypeCallMatrix hdf5GenoMat = new HDF5GenotypeCallMatrix(hdf5Writer);
                AbstractGenotypeCallMatrix.copyGenoMatrix(genoMat, hdf5GenoMat);
                hdf5Writer.close();
            }
        } catch (ParseException ex) {
            HelpFormatter helpFormatter = new HelpFormatter();
            helpFormatter.printHelp("fftohdf5", options);

            System.exit(-1);
        }
    }
}