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improve BED support per hts-specs version 1.0 specification
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186 changes: 123 additions & 63 deletions
186
feature/src/main/java/org/dishevelled/bio/feature/bed/BedRecord.java
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179 changes: 179 additions & 0 deletions
179
tools/src/main/java/org/dishevelled/bio/tools/Gff3ToBed.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,179 @@ | ||
| /* | ||
| dsh-bio-tools Command line tools. | ||
| Copyright (c) 2013-2024 held jointly by the individual authors. | ||
| 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.fsf.org/licensing/licenses/lgpl.html | ||
| > http://www.opensource.org/licenses/lgpl-license.php | ||
| */ | ||
| package org.dishevelled.bio.tools; | ||
|
|
||
| import static org.dishevelled.compress.Readers.reader; | ||
| import static org.dishevelled.compress.Writers.writer; | ||
|
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| import java.io.BufferedReader; | ||
| import java.io.File; | ||
| import java.io.PrintWriter; | ||
|
|
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| import java.nio.file.Path; | ||
|
|
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| import java.util.List; | ||
|
|
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| import java.util.concurrent.Callable; | ||
|
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| import org.dishevelled.bio.feature.gff3.Gff3Listener; | ||
| import org.dishevelled.bio.feature.gff3.Gff3Reader; | ||
| import org.dishevelled.bio.feature.gff3.Gff3Record; | ||
|
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| import org.dishevelled.bio.feature.bed.BedRecord; | ||
| import org.dishevelled.bio.feature.bed.BedWriter; | ||
|
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| 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; | ||
|
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| import org.dishevelled.commandline.argument.FileArgument; | ||
| import org.dishevelled.commandline.argument.PathArgument; | ||
|
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| /** | ||
| * Convert transcript features in GFF3 format to BED format. | ||
| * | ||
| * @since 2.4 | ||
| * @author Michael Heuer | ||
| */ | ||
| public final class Gff3ToBed implements Callable<Integer> { | ||
| private final Path inputGff3Path; | ||
| private final File outputBedFile; | ||
| private static final String USAGE = "dsh-gff3-to-bed [args]"; | ||
|
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| public Gff3ToBed(final Path inputGff3Path, final File outputBedFile) { | ||
| this.inputGff3Path = inputGff3Path; | ||
| this.outputBedFile = outputBedFile; | ||
| } | ||
|
|
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| @Override | ||
| public Integer call() throws Exception { | ||
| BufferedReader reader = null; | ||
| PrintWriter writer = null; | ||
| try { | ||
| reader = reader(inputGff3Path); | ||
| writer = writer(outputBedFile); | ||
|
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| final PrintWriter w = writer; | ||
| Gff3Reader.stream(reader, new Gff3Listener() { | ||
| @Override | ||
| public boolean record(final Gff3Record gff3Record) { | ||
| if (accept(gff3Record)) { | ||
| BedRecord bedRecord = convert(gff3Record); | ||
| BedWriter.write(bedRecord, w); | ||
| } | ||
| return true; | ||
| } | ||
| }); | ||
|
|
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| return 0; | ||
| } | ||
| finally { | ||
| try { | ||
| reader.close(); | ||
| } | ||
| catch (Exception e) { | ||
| // ignore | ||
| } | ||
| try { | ||
| writer.close(); | ||
| } | ||
| catch (Exception e) { | ||
| // ignore | ||
| } | ||
| } | ||
| } | ||
|
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| static boolean accept(final Gff3Record gff3Record) { | ||
| return gff3Record.getAttributes().containsKey("transcript_id"); | ||
| } | ||
|
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| static BedRecord convert(final Gff3Record gff3Record) { | ||
| String chrom = gff3Record.getSeqid(); | ||
| long chromStart = gff3Record.getStart(); | ||
| long chromEnd = gff3Record.getEnd(); | ||
|
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| // transcript_id is present, but might be multi-valued | ||
| List<String> transcriptIds = gff3Record.getAttributes().get("transcript_id"); | ||
| String transcriptId = transcriptIds.get(0); | ||
|
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| // score may not be present | ||
| int score = gff3Record.getScore() == null ? 0 : Math.max(0, Math.min(1000, (int) Math.round(gff3Record.getScore()))); | ||
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| String strand = gff3Record.getStrand() == null ? "." : gff3Record.getStrand(); | ||
| long thickStart = chromStart; | ||
| long thickEnd = chromEnd; | ||
| String itemRgb = "0"; | ||
|
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| // at least one block must be present | ||
| int blockCount = 1; | ||
| long[] blockSizes = new long[] { (chromEnd - chromStart) }; | ||
| long[] blockStarts = new long[] { 0L }; | ||
|
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| return new BedRecord(chrom, chromStart, chromEnd, transcriptId, score, strand, thickStart, thickEnd, itemRgb, blockCount, blockSizes, blockStarts); | ||
| } | ||
|
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| /** | ||
| * 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"); | ||
| PathArgument inputGff3Path = new PathArgument("i", "input-gff3-path", "input GFF3 path, default stdin", false); | ||
| FileArgument outputBedFile = new FileArgument("o", "output-bed-file", "output BED file, default stdout", false); | ||
|
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| ArgumentList arguments = new ArgumentList(about, help, inputGff3Path, outputBedFile); | ||
| CommandLine commandLine = new CommandLine(args); | ||
|
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| Gff3ToBed gff3ToBed = 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); | ||
| } | ||
| gff3ToBed = new Gff3ToBed(inputGff3Path.getValue(), outputBedFile.getValue()); | ||
| } | ||
| catch (CommandLineParseException e) { | ||
| Usage.usage(USAGE, e, commandLine, arguments, System.err); | ||
| System.exit(-1); | ||
| } | ||
| try { | ||
| System.exit(gff3ToBed.call()); | ||
| } | ||
| catch (Exception e) { | ||
| e.printStackTrace(); | ||
| System.exit(1); | ||
| } | ||
| } | ||
| } |
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