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Next generation sequencing (NGS/HTS) command line tools.
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/*
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.checkArgument;
import static com.google.common.base.Preconditions.checkNotNull;
import static org.dishevelled.compress.Writers.writer;
import java.io.File;
import java.io.PrintWriter;
import java.util.concurrent.Callable;
import org.apache.commons.math3.distribution.IntegerDistribution;
import org.apache.commons.math3.distribution.NormalDistribution;
import org.apache.commons.math3.distribution.RealDistribution;
import org.apache.commons.math3.distribution.UniformIntegerDistribution;
import org.apache.commons.math3.random.MersenneTwister;
import org.apache.commons.math3.random.RandomGenerator;
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.dishevelled.commandline.argument.StringArgument;
import org.nmdp.ngs.align.BedRecord;
import org.nmdp.ngs.align.BedWriter;
/**
* Generate records in BED format.
*/
public final class GenerateBed implements Callable {
private final File bedFile;
private final int n;
private final int size;
private final String chrom;
private final RandomGenerator random;
private final RealDistribution length;
private final IntegerDistribution location;
private static final int DEFAULT_N = 1000;
private static final int DEFAULT_SIZE = 100000;
private static final String DEFAULT_CHROM = "1";
private static final double NO_VARIATION = 1.0E-100;
private static final double DEFAULT_MEAN_LENGTH = 100.0d;
private static final double DEFAULT_LENGTH_VARIATION = 10.0d;
private static final String USAGE = "ngs-generate-bed [args]";
/**
* Generate records in BED format.
*
* @param bedFile output BED file, if any
* @param n number of BED records to generate, must be at least zero
* @param size chromosome size, must be at least zero
* @param chrom chromosome name, must not be null
* @param random random generator, must not be null
* @param length length distribution, must not be null
*/
public GenerateBed(final File bedFile, final int n, final int size, final String chrom, final RandomGenerator random, final RealDistribution length) {
checkArgument(n >= 0, "n must be at least zero");
checkArgument(size >= 0, "size must be at least zero");
checkNotNull(chrom);
checkNotNull(random);
checkNotNull(length);
this.bedFile = bedFile;
this.n = n;
this.size = size;
this.chrom = chrom;
this.random = random;
this.length = length;
int flanking = (int) (length.getNumericalMean() + length.getNumericalVariance());
location = new UniformIntegerDistribution(this.random, 1 - flanking, size + flanking);
}
@Override
public Integer call() throws Exception {
PrintWriter writer = null;
try {
writer = writer(bedFile);
for (int i = 0; i < n; i++) {
// sample location and length
long start = (long) location.sample();
long end = start + 1L + (long) length.sample();
// trim to chrom ends
long adjStart = Math.min((long) (size - 1), Math.max(0L, start));
long adjEnd = Math.max(adjStart + 1L, Math.min((long) (size - 1), end));
// and write
BedWriter.write(new BedRecord(chrom, adjStart, adjEnd, "record" + i, "0", "+"), writer);
}
return 0;
}
finally {
try {
writer.close();
}
catch (Exception e) {
// ignore
}
}
}
/**
* Main.
*
* @param args command line arguments
*/
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 bedFile = new FileArgument("o", "bed-file", "output BED file, default stdout", false);
IntegerArgument n = new IntegerArgument("n", "n", "number of BED records to generate, default " + DEFAULT_N, false);
IntegerArgument size = new IntegerArgument("s", "size", "chromosome size, default " + DEFAULT_SIZE, false);
StringArgument chrom = new StringArgument("c", "chrom", "chromosome name, default " + DEFAULT_CHROM, false);
DoubleArgument meanLength = new DoubleArgument("l", "mean-length", "mean length, default " + DEFAULT_MEAN_LENGTH, false);
DoubleArgument lengthVariation = new DoubleArgument("v", "length-variation", "length variation, default " + DEFAULT_LENGTH_VARIATION, false);
IntegerArgument seed = new IntegerArgument("z", "seed", "random number seed, default relates to current time", false);
ArgumentList arguments = new ArgumentList(about, help, bedFile, n, size, chrom, meanLength, lengthVariation, seed);
CommandLine commandLine = new CommandLine(args);
GenerateBed generateBed = 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();
double lv = Math.max(NO_VARIATION, lengthVariation.getValue(DEFAULT_LENGTH_VARIATION));
RealDistribution length = new NormalDistribution(random, meanLength.getValue(DEFAULT_MEAN_LENGTH), lv, NormalDistribution.DEFAULT_INVERSE_ABSOLUTE_ACCURACY);
generateBed = new GenerateBed(bedFile.getValue(), n.getValue(DEFAULT_N), size.getValue(DEFAULT_SIZE), chrom.getValue(DEFAULT_CHROM), random, length);
}
catch (CommandLineParseException e) {
Usage.usage(USAGE, e, commandLine, arguments, System.err);
System.exit(-1);
}
try {
System.exit(generateBed.call());
}
catch (Exception e) {
e.printStackTrace();
System.exit(1);
}
}
}