fr.ens.transcriptome.aozan.fastqscreen.FastqScreen.java Source code

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Here is the source code for fr.ens.transcriptome.aozan.fastqscreen.FastqScreen.java

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/*
 *                  Aozan development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU General Public License version 3 or later 
 * and CeCILL. This should be distributed with the code. If you 
 * do not have a copy, see:
 *
 *      http://www.gnu.org/licenses/gpl-3.0-standalone.html
 *      http://www.cecill.info/licences/Licence_CeCILL_V2-en.html
 *
 * Copyright for this code is held jointly by the Genomic platform
 * of the Institut de Biologie de l'cole Normale Suprieure and
 * the individual authors. These should be listed in @author doc
 * comments.
 *
 * For more information on the Aozan project and its aims,
 * or to join the Aozan Google group, visit the home page at:
 *
 *      http://www.transcriptome.ens.fr/aozan
 *
 */

package fr.ens.transcriptome.aozan.fastqscreen;

import static fr.ens.transcriptome.eoulsan.util.StringUtils.toTimeHumanReadable;

import java.io.File;
import java.io.IOException;
import java.util.List;
import java.util.Properties;
import java.util.concurrent.TimeUnit;
import java.util.logging.Logger;

import com.google.common.base.Stopwatch;

import fr.ens.transcriptome.aozan.AozanException;
import fr.ens.transcriptome.aozan.Common;
import fr.ens.transcriptome.aozan.QC;
import fr.ens.transcriptome.aozan.Settings;
import fr.ens.transcriptome.aozan.io.FastqSample;
import fr.ens.transcriptome.eoulsan.EoulsanRuntime;

/**
 * This class execute fastqscreen pair-end mode or single-end.
 * @since 1.0
 * @author Sandrine Perrin
 */
public class FastqScreen {

    /** Logger. */
    private static final Logger LOGGER = Common.getLogger();

    private final String tmpDir;
    private int confThreads;
    private final String mapperName;
    private final String mapperArgument;

    /**
     * Mode pair-end : execute fastqscreen.
     * @param fastqRead fastq file input for mapper
     * @param fastqSample instance to describe fastq sample
     * @param genomes list or reference genome, used by mapper
     * @param genomeSample genome reference corresponding to sample
     * @return FastqScreenResult object contains results for each reference genome
     * @throws AozanException
     */
    public FastqScreenResult execute(final File fastqRead, final FastqSample fastqSample,
            final List<String> genomes, final String genomeSample, final boolean paired) throws AozanException {

        return this.execute(fastqRead, null, fastqSample, genomes, genomeSample, paired);

    }

    /**
     * Mode single-end : execute fastqscreen.
     * @param fastqRead1 fastq read1 file input for mapper
     * @param fastqRead2 fastq read2 file input for mapper
     * @param fastqSample instance to describe fastq sample
     * @param genomes list or reference genome, used by mapper
     * @param genomeSample genome reference corresponding to sample
     * @param isPairedMode true if a pair-end run and option paired mode equals
     *          true else false
     * @throws AozanException
     */
    public FastqScreenResult execute(final File fastqRead1, final File fastqRead2, final FastqSample fastqSample,
            final List<String> genomes, final String genomeSample, final boolean isPairedMode)
            throws AozanException {

        // Timer
        final Stopwatch timer = Stopwatch.createStarted();

        final FastqScreenPseudoMapReduce pmr = new FastqScreenPseudoMapReduce(this.tmpDir, isPairedMode,
                this.mapperName, this.mapperArgument);

        try {

            if (isPairedMode) {
                pmr.doMap(fastqRead1, fastqRead2, genomes, genomeSample, this.confThreads);
            } else {
                pmr.doMap(fastqRead1, genomes, genomeSample, this.confThreads);
            }

            LOGGER.fine("FASTQSCREEN : step map for " + fastqSample.getKeyFastqSample() + " in mode "
                    + (isPairedMode ? "paired" : "single") + " on genome(s) " + genomes + " in "
                    + toTimeHumanReadable(timer.elapsed(TimeUnit.MILLISECONDS)));

            timer.reset();
            timer.start();

            pmr.doReduce(new File(this.tmpDir + "/outputDoReduce.txt"));

            LOGGER.fine("FASTQSCREEN : step reduce for " + fastqSample.getKeyFastqSample() + " in mode "
                    + (isPairedMode ? "paired" : "single") + " in "
                    + toTimeHumanReadable(timer.elapsed(TimeUnit.MILLISECONDS)));

            // Remove temporary output file use in map-reduce step
            final File f = new File(this.tmpDir + "/outputDoReduce.txt");
            if (!f.delete()) {
                LOGGER.warning("Fastqscreen : fail to delete file " + f.getAbsolutePath());
            }

        } catch (final IOException e) {
            throw new AozanException(e);

        } finally {
            timer.stop();
        }

        return pmr.getFastqScreenResult();
    }

    //
    // Constructor
    //

    /**
     * Public constructor of fastqscreen. Initialization of settings of Eoulsan
     * necessary for use of mapper index.
     * @param properties properties defines in configuration of aozan
     */
    public FastqScreen(final Properties properties) {

        this.tmpDir = properties.getProperty(QC.TMP_DIR);

        if (properties.containsKey(Settings.QC_CONF_THREADS_KEY)) {
            try {
                this.confThreads = Integer.parseInt(properties.getProperty(Settings.QC_CONF_THREADS_KEY));
            } catch (final Exception e) {
            }
        }

        // Parameter mapper instead of default value
        this.mapperName = properties.getProperty(Settings.QC_CONF_FASTQSCREEN_MAPPER_KEY);
        this.mapperArgument = properties.getProperty(Settings.QC_CONF_FASTQSCREEN_MAPPER_ARGUMENT_KEY);

        final fr.ens.transcriptome.eoulsan.Settings settings = EoulsanRuntime.getSettings();

        settings.setGenomeDescStoragePath(
                properties.getProperty(Settings.QC_CONF_FASTQSCREEN_SETTINGS_GENOMES_DESC_PATH_KEY));
        settings.setGenomeMapperIndexStoragePath(
                properties.getProperty(Settings.QC_CONF_FASTQSCREEN_SETTINGS_MAPPERS_INDEXES_PATH_KEY));
        settings.setGenomeStoragePath(properties.getProperty(Settings.QC_CONF_FASTQSCREEN_SETTINGS_GENOMES_KEY));

    }
}