/*
* Eoulsan development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public License version 2.1 or
* later and CeCILL-C. This should be distributed with the code.
* If you do not have a copy, see:
*
* http://www.gnu.org/licenses/lgpl-2.1.txt
* http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.txt
*
* Copyright for this code is held jointly by the Genomic platform
* of the Institut de Biologie de l'École normale supérieure and
* the individual authors. These should be listed in @author doc
* comments.
*
* For more information on the Eoulsan project and its aims,
* or to join the Eoulsan Google group, visit the home page
* at:
*
* http://outils.genomique.biologie.ens.fr/eoulsan
*
*/
package fr.ens.biologie.genomique.eoulsan.modules.generators;
import static fr.ens.biologie.genomique.eoulsan.EoulsanLogger.getLogger;
import static fr.ens.biologie.genomique.eoulsan.core.InputPortsBuilder.singleInputPort;
import static fr.ens.biologie.genomique.eoulsan.core.OutputPortsBuilder.singleOutputPort;
import static fr.ens.biologie.genomique.eoulsan.data.DataFormats.ANNOTATION_GFF;
import static fr.ens.biologie.genomique.eoulsan.data.DataFormats.GENOME_FASTA;
import java.io.IOException;
import fr.ens.biologie.genomique.eoulsan.Globals;
import fr.ens.biologie.genomique.eoulsan.bio.Sequence;
import fr.ens.biologie.genomique.eoulsan.bio.io.FastaWriter;
import fr.ens.biologie.genomique.eoulsan.bio.io.GFFFastaReader;
import fr.ens.biologie.genomique.eoulsan.bio.io.SequenceReader;
import fr.ens.biologie.genomique.eoulsan.bio.io.SequenceWriter;
import fr.ens.biologie.genomique.eoulsan.core.InputPorts;
import fr.ens.biologie.genomique.eoulsan.core.OutputPorts;
import fr.ens.biologie.genomique.eoulsan.core.TaskContext;
import fr.ens.biologie.genomique.eoulsan.core.TaskResult;
import fr.ens.biologie.genomique.eoulsan.core.TaskStatus;
import fr.ens.biologie.genomique.eoulsan.core.Version;
import fr.ens.biologie.genomique.eoulsan.data.Data;
import fr.ens.biologie.genomique.eoulsan.data.DataFile;
import fr.ens.biologie.genomique.eoulsan.modules.AbstractModule;
/**
* This generator allow to generate a genome fasta file from the fasta section
* of a GFF file.
* @since 1.1
* @author Laurent Jourdren
*/
public class GFFFastaGeneratorModule extends AbstractModule {
public static final String MODULE_NAME = "gfffastagenerator";
@Override
public String getName() {
return "gfffastagenerator";
}
@Override
public String getDescription() {
return "Generate Genome Fasta file from a Fasta section of GFF file";
}
@Override
public Version getVersion() {
return Globals.APP_VERSION;
}
@Override
public InputPorts getInputPorts() {
return singleInputPort(ANNOTATION_GFF);
}
@Override
public OutputPorts getOutputPorts() {
return singleOutputPort(GENOME_FASTA);
}
@Override
public TaskResult execute(final TaskContext context,
final TaskStatus status) {
try {
// Get input and output data
final Data inData = context.getInputData(ANNOTATION_GFF);
final Data outData = context.getOutputData(GENOME_FASTA, inData);
// Get the annotation DataFile
final DataFile annotationDataFile = inData.getDataFile();
// Get the output DataFile
final DataFile genomeDataFile = outData.getDataFile();
getLogger().info("Input annotation file: " + annotationDataFile);
getLogger().info("Output genome file: " + genomeDataFile);
final SequenceReader reader =
new GFFFastaReader(annotationDataFile.open());
final SequenceWriter writer = new FastaWriter(genomeDataFile.create());
for (final Sequence sequence : reader) {
writer.write(sequence);
}
reader.throwException();
reader.close();
writer.close();
} catch (IOException e) {
return status.createTaskResult(e);
}
status.setProgressMessage("Genome fasta creation");
return status.createTaskResult();
}
}