Java tutorial
/* ngs-tools Next generation sequencing (NGS/HTS) command line tools. Copyright (c) 2014-2015 National Marrow Donor Program (NMDP) This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version. This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; with out even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. You should have received a copy of the GNU Lesser General Public License along with this library; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA. > http://www.gnu.org/licenses/lgpl.html */ package org.nmdp.ngs.tools; import static com.google.common.base.Preconditions.checkNotNull; import static org.dishevelled.compress.Readers.reader; import static org.dishevelled.compress.Writers.writer; import java.io.BufferedReader; import java.io.File; import java.io.PrintWriter; import java.io.IOException; import java.util.concurrent.Callable; import org.apache.commons.math3.distribution.BinomialDistribution; import org.apache.commons.math3.random.MersenneTwister; import org.apache.commons.math3.random.RandomGenerator; import org.biojava.bio.program.fastq.Fastq; import org.biojava.bio.program.fastq.FastqWriter; import org.biojava.bio.program.fastq.SangerFastqWriter; import org.dishevelled.commandline.ArgumentList; import org.dishevelled.commandline.CommandLine; import org.dishevelled.commandline.CommandLineParseException; import org.dishevelled.commandline.CommandLineParser; import org.dishevelled.commandline.Switch; import org.dishevelled.commandline.Usage; import org.dishevelled.commandline.argument.DoubleArgument; import org.dishevelled.commandline.argument.FileArgument; import org.dishevelled.commandline.argument.IntegerArgument; import org.nmdp.ngs.reads.paired.PairedEndAdapter; import org.nmdp.ngs.reads.paired.PairedEndFastqReader; /** * Downsample sequences from a file in interleaved FASTQ format. */ public final class DownsampleInterleavedFastq implements Callable<Integer> { private final File inputFastqFile; private final File outputFastqFile; private final BinomialDistribution distribution; private final FastqWriter fastqWriter = new SangerFastqWriter(); private static final String USAGE = "ngs-downsample-interleaved-fastq -p 0.5 [args]"; /** * Downsample sequences from a file in interleaved FASTQ format. * * @param inputFastqFile input interleaved FASTQ file, if any * @param outputFastqFile output interleaved FASTQ file, if any * @param distribution binomial distribution, must not be null */ public DownsampleInterleavedFastq(final File inputFastqFile, final File outputFastqFile, final BinomialDistribution distribution) { checkNotNull(distribution); this.inputFastqFile = inputFastqFile; this.outputFastqFile = outputFastqFile; this.distribution = distribution; } @Override public Integer call() throws Exception { BufferedReader reader = null; PrintWriter writer = null; try { reader = reader(inputFastqFile); writer = writer(outputFastqFile); final PrintWriter w = writer; PairedEndFastqReader.streamInterleaved(reader, new PairedEndAdapter() { @Override public void paired(final Fastq left, final Fastq right) { if (distribution.sample() > 0) { try { fastqWriter.append(w, left); fastqWriter.append(w, right); } catch (IOException e) { throw new RuntimeException("could not write FASTQ", e); } } } }); return 0; } finally { try { reader.close(); } catch (Exception e) { // ignore } try { writer.close(); } catch (Exception e) { // ignore } } } /** * Main. * * @param args command line args */ public static void main(final String[] args) { Switch about = new Switch("a", "about", "display about message"); Switch help = new Switch("h", "help", "display help message"); FileArgument inputFastqFile = new FileArgument("i", "input-fastq-file", "input interleaved FASTQ file, default stdin", false); FileArgument outputFastqFile = new FileArgument("o", "output-fastq-file", "output interleaved FASTQ file, default stdout", false); DoubleArgument probability = new DoubleArgument("p", "probability", "probability a FASTQ record will be removed, [0.0-1.0]", true); IntegerArgument seed = new IntegerArgument("z", "seed", "random number seed, default relates to current time", false); ArgumentList arguments = new ArgumentList(about, help, inputFastqFile, outputFastqFile, probability, seed); CommandLine commandLine = new CommandLine(args); DownsampleInterleavedFastq downsampleInterleavedFastq = null; try { CommandLineParser.parse(commandLine, arguments); if (about.wasFound()) { About.about(System.out); System.exit(0); } if (help.wasFound()) { Usage.usage(USAGE, null, commandLine, arguments, System.out); System.exit(0); } RandomGenerator random = seed.wasFound() ? new MersenneTwister(seed.getValue()) : new MersenneTwister(); BinomialDistribution distribution = new BinomialDistribution(random, 1, probability.getValue()); downsampleInterleavedFastq = new DownsampleInterleavedFastq(inputFastqFile.getValue(), outputFastqFile.getValue(), distribution); } catch (CommandLineParseException e) { if (about.wasFound()) { About.about(System.out); System.exit(0); } if (help.wasFound()) { Usage.usage(USAGE, null, commandLine, arguments, System.out); System.exit(0); } Usage.usage(USAGE, e, commandLine, arguments, System.err); System.exit(-1); } catch (IllegalArgumentException e) { Usage.usage(USAGE, e, commandLine, arguments, System.err); System.exit(-1); } try { System.exit(downsampleInterleavedFastq.call()); } catch (Exception e) { e.printStackTrace(); System.exit(1); } } }