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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 static org.nmdp.ngs.hml.HmlUtils.toDnaSymbolList;
import java.io.BufferedReader;
import java.io.File;
import java.io.PrintWriter;
import java.util.concurrent.Callable;
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.nmdp.ngs.hml.HmlReader;
import org.nmdp.ngs.hml.jaxb.ConsensusSequence;
import org.nmdp.ngs.hml.jaxb.ConsensusSequenceBlock;
import org.nmdp.ngs.hml.jaxb.Hml;
import org.nmdp.ngs.hml.jaxb.ReferenceDatabase;
import org.nmdp.ngs.hml.jaxb.Sample;
import org.nmdp.ngs.hml.jaxb.Typing;
/**
* Extract consensus sequences from a file in HML format.
*/
public final class ExtractConsensus implements Callable {
private final File inputHmlFile;
private static final String USAGE = "ngs-extract-consensus [args]";
/**
* Extract consensus sequences from a file in HML format.
*
* @param inputHmlFile input HML file, if any
*/
public ExtractConsensus(final File inputHmlFile) {
this.inputHmlFile = inputHmlFile;
}
@Override
public Integer call() throws Exception {
BufferedReader reader = null;
try {
reader = reader(inputHmlFile);
Hml hml = HmlReader.read(reader);
for (Sample sample : hml.getSample()) {
String id = sample.getId();
int typingCount = 0;
for (Typing typing : sample.getTyping()) {
typingCount++;
for (ConsensusSequence consensusSequence : typing.getConsensusSequence()) {
int cons = 0;
try (PrintWriter writer = writer(new File(id + "_" + typingCount + "_" + cons + ".fa.gz"))) {
int blocks = 0;
for (ConsensusSequenceBlock consensusSequenceBlock : consensusSequence.getConsensusSequenceBlock()) {
StringBuilder sb = new StringBuilder(1200);
sb.append(">");
sb.append(blocks);
sb.append("|");
sb.append(((ReferenceDatabase.ReferenceSequence) consensusSequenceBlock.getReferenceSequenceId()).getId());
sb.append("|");
sb.append(consensusSequenceBlock.getStart() == null ? "" : consensusSequenceBlock.getStart());
sb.append("|");
sb.append(consensusSequenceBlock.getPhasingGroup() == null ? "" : consensusSequenceBlock.getPhasingGroup());
sb.append("|");
sb.append(consensusSequenceBlock.getExpectedCopyNumber() == null ? "" : consensusSequenceBlock.getExpectedCopyNumber());
sb.append("|");
sb.append(consensusSequenceBlock.getVariant().isEmpty() ? "1" : "0");
sb.append("|");
sb.append((consensusSequenceBlock.isContinuity() != null && consensusSequenceBlock.isContinuity().booleanValue()) ? "1" : "0");
sb.append("\n");
sb.append(toDnaSymbolList(consensusSequenceBlock.getSequence()).seqString());
writer.println(sb.toString());
blocks++;
}
}
cons++;
}
}
}
return 0;
}
finally {
try {
reader.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 inputHmlFile = new FileArgument("i", "input-hml-file", "input HML file, default stdin", false);
ArgumentList arguments = new ArgumentList(about, help, inputHmlFile);
CommandLine commandLine = new CommandLine(args);
ExtractConsensus extractConsensus = 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);
}
extractConsensus = new ExtractConsensus(inputHmlFile.getValue());
}
catch (CommandLineParseException | IllegalArgumentException e) {
Usage.usage(USAGE, e, commandLine, arguments, System.err);
System.exit(-1);
}
try {
System.exit(extractConsensus.call());
}
catch (Exception e) {
e.printStackTrace();
System.exit(1);
}
}
}