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Next generation sequencing (NGS/HTS) command line tools.
/*
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 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.util.concurrent.Callable;
import com.google.common.base.Joiner;
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.FileArgument;
import org.dishevelled.commandline.argument.StringArgument;
import org.nmdp.ngs.align.BedRecord;
import org.nmdp.ngs.align.BedWriter;
import org.nmdp.ngs.align.HighScoringPair;
import org.nmdp.ngs.align.HspListener;
import org.nmdp.ngs.align.HspReader;
/**
* Convert HSPs to BED format.
*/
public final class HspToBed implements Callable {
private final String displayName;
private final File hspFile;
private final File bedFile;
private final boolean reverse;
private final boolean transformEvalue;
private static final String USAGE = "ngs-hsp-to-bed [args]";
/**
* Convert HSPs to BED format.
*
* @param displayName query display name, if any
* @param hspFile input HSP file, from e.g. blastn -outfmt 7, if any
* @param bedFile output BED file, if any
* @param reverse true to reverse query and target in BED file
* @param transformEvalue true to transform e-value to BED score [0..1000]
*/
public HspToBed(final String displayName, final File hspFile, final File bedFile, final boolean reverse, final boolean transformEvalue) {
this.displayName = displayName;
this.hspFile = hspFile;
this.bedFile = bedFile;
this.reverse = reverse;
this.transformEvalue = transformEvalue;
}
@Override
public Integer call() throws Exception {
BufferedReader reader = null;
PrintWriter writer = null;
try {
reader = reader(hspFile);
writer = writer(bedFile);
final PrintWriter w = writer;
HspReader.stream(reader, new HspListener() {
@Override
public boolean hsp(final HighScoringPair hsp) {
BedWriter.write((reverse ? toReverseBedRecord(hsp) : toBedRecord(hsp)), w);
return true;
}
});
return 0;
}
finally {
try {
reader.close();
}
catch (Exception e) {
// empty
}
try {
writer.close();
}
catch (Exception e) {
// empty
}
}
}
private BedRecord toBedRecord(final HighScoringPair hsp) {
String chrom = hsp.target();
// hsps are 1-based, fully closed; bed records are 0-based, closed open
long start = hsp.targetStart() - 1L;
long end = hsp.targetEnd();
String name = Joiner.on(":").join((displayName != null ? displayName : hsp.source()), hsp.sourceStart(), hsp.sourceEnd(), (hsp.sourceStart() <= hsp.sourceEnd() ? "+" : "-"), hsp.percentIdentity(), hsp.alignmentLength(), hsp.mismatches(), hsp.gapOpens(), hsp.evalue(), hsp.bitScore());
String score = String.valueOf((transformEvalue ? transform(hsp.evalue()) : hsp.evalue()));
String strand = hsp.targetStart() <= hsp.targetEnd() ? "+" : "-";
return new BedRecord(chrom, start, end, name, score, strand);
}
private BedRecord toReverseBedRecord(final HighScoringPair hsp) {
String chrom = displayName != null ? displayName : hsp.source();
// hsps are 1-based, fully closed; bed records are 0-based, closed open
long start = hsp.sourceStart() - 1L;
long end = hsp.sourceEnd();
String name = Joiner.on(":").join(hsp.target(), hsp.targetStart(), hsp.targetEnd(), (hsp.targetStart() <= hsp.targetEnd() ? "+" : "-"), hsp.percentIdentity(), hsp.alignmentLength(), hsp.mismatches(), hsp.gapOpens(), hsp.evalue(), hsp.bitScore());
String score = String.valueOf((transformEvalue ? transform(hsp.evalue()) : hsp.evalue()));
String strand = hsp.sourceStart() <= hsp.sourceEnd() ? "+" : "-";
return new BedRecord(chrom, start, end, name, score, strand);
}
private static int transform(final double evalue) {
double transformedEvalue = -Math.log10(evalue) + 2.0d;
if (Double.isInfinite(transformedEvalue)) {
transformedEvalue = 257.0d; // 255.0 + 2.0d
}
transformedEvalue = lerp(transformedEvalue, 0.0d, 257.0d, 0.0d, 1000.0d);
return (int) transformedEvalue;
}
private static double lerp(final double value, final double sourceMinimum, final double sourceMaximum, final double targetMinimum, final double targetMaximum) {
return targetMinimum + (targetMaximum - targetMinimum) * ((value - sourceMinimum) / (sourceMaximum - sourceMinimum));
}
/**
* 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");
StringArgument displayName = new StringArgument("d", "display-name", "query display name", false);
FileArgument hspFile = new FileArgument("i", "hsp-file", "input HSP file, from e.g. blastn -outfmt 7, default stdin", false);
FileArgument bedFile = new FileArgument("o", "bed-file", "output BED file, default stdout", false);
Switch reverse = new Switch("r", "reverse", "reverse query and target in BED file");
Switch transformEvalue = new Switch("t", "transform-evalue", "transform e-value to BED score [0..1000]");
ArgumentList arguments = new ArgumentList(about, help, displayName, hspFile, bedFile, reverse, transformEvalue);
CommandLine commandLine = new CommandLine(args);
HspToBed hspToBed = 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);
}
hspToBed = new HspToBed(displayName.getValue(), hspFile.getValue(), bedFile.getValue(), reverse.wasFound(), transformEvalue.wasFound());
}
catch (CommandLineParseException e) {
Usage.usage(USAGE, e, commandLine, arguments, System.err);
System.exit(-1);
}
try {
System.exit(hspToBed.call());
}
catch (Exception e) {
e.printStackTrace();
System.exit(1);
}
}
}