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adding remap-phase-set command line tool
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tools/src/main/java/org/dishevelled/bio/tools/RemapPhaseSet.java
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| Original file line number | Diff line number | Diff line change |
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| /* | ||
| dsh-bio-tools Command line tools. | ||
| Copyright (c) 2013-2017 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 com.google.common.base.Preconditions.checkNotNull; | ||
|
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| import static org.dishevelled.compress.Readers.reader; | ||
| import static org.dishevelled.compress.Writers.writer; | ||
|
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| import java.io.File; | ||
| import java.io.PrintWriter; | ||
|
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| import java.util.ArrayList; | ||
| import java.util.HashMap; | ||
| import java.util.List; | ||
| import java.util.Map; | ||
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| import java.util.concurrent.Callable; | ||
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| import com.google.common.collect.ArrayListMultimap; | ||
| import com.google.common.collect.ImmutableList; | ||
| import com.google.common.collect.ListMultimap; | ||
|
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| import org.dishevelled.bio.variant.vcf.VcfGenotype; | ||
| import org.dishevelled.bio.variant.vcf.VcfHeader; | ||
| import org.dishevelled.bio.variant.vcf.VcfReader; | ||
| import org.dishevelled.bio.variant.vcf.VcfRecord; | ||
| import org.dishevelled.bio.variant.vcf.VcfSample; | ||
| import org.dishevelled.bio.variant.vcf.VcfWriter; | ||
| import org.dishevelled.bio.variant.vcf.VcfStreamAdapter; | ||
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| import org.dishevelled.bio.variant.vcf.header.VcfHeaderLineType; | ||
| import org.dishevelled.bio.variant.vcf.header.VcfHeaderLines; | ||
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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; | ||
|
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| /** | ||
| * Remap Type=String PS phase set ids in VCF format to Type=Integer. | ||
| * | ||
| * @author Michael Heuer | ||
| */ | ||
| public final class RemapPhaseSet implements Callable<Integer> { | ||
| private final File inputVcfFile; | ||
| private final File outputVcfFile; | ||
| private static final String USAGE = "dsh-remap-phase-set -i input.vcf.gz -o output.vcf.gz"; | ||
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|
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| /** | ||
| * Remap Type=String PS phase set ids in VCF format to Type=Integer. | ||
| * | ||
| * @param inputVcfFile input VCF file, if any | ||
| * @param outputVcfFile output VCF file, if any | ||
| */ | ||
| public RemapPhaseSet(final File inputVcfFile, final File outputVcfFile) { | ||
| this.inputVcfFile = inputVcfFile; | ||
| this.outputVcfFile = outputVcfFile; | ||
| } | ||
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|
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| @Override | ||
| public Integer call() throws Exception { | ||
| PrintWriter writer = null; | ||
| try { | ||
| writer = writer(outputVcfFile); | ||
|
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| final PrintWriter w = writer; | ||
| VcfReader.stream(reader(inputVcfFile), new VcfStreamAdapter() { | ||
| private boolean wroteSamples = false; | ||
| private boolean remapPhaseSet = false; | ||
| private List<VcfSample> samples = new ArrayList<VcfSample>(); | ||
| private int phaseSetId = 0; | ||
| private Map<String, Integer> phaseSetIds = new HashMap<String, Integer>(); | ||
|
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| @Override | ||
| public void header(final VcfHeader header) { | ||
| VcfHeaderLines headerLines = VcfHeaderLines.fromHeader(header); | ||
| if (headerLines.getFormatHeaderLines().containsKey("PS") && | ||
| VcfHeaderLineType.String.equals(headerLines.getFormatHeaderLines().get("PS").getType())) { | ||
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| remapPhaseSet = true; | ||
| VcfHeader.Builder builder = VcfHeader.builder().withFileFormat(header.getFileFormat()); | ||
| for (String meta : header.getMeta()) { | ||
| if (meta.startsWith("##FORMAT=<ID=PS")) { | ||
| String description = headerLines.getFormatHeaderLines().get("PS").getDescription() + " (converted from Type=String to Type=Integer)"; | ||
| builder.withMeta("##FORMAT=<ID=PS,Number=1,Type=Integer,Description=\"" + description + "\">"); | ||
| } | ||
| else { | ||
| builder.withMeta(meta); | ||
| } | ||
| } | ||
| VcfWriter.writeHeader(builder.build(), w); | ||
| } | ||
| else { | ||
| VcfWriter.writeHeader(header, w); | ||
| } | ||
| } | ||
|
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| @Override | ||
| public void sample(final VcfSample sample) { | ||
| samples.add(sample); | ||
| } | ||
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| @Override | ||
| public void record(final VcfRecord record) { | ||
| // write out samples | ||
| if (!wroteSamples) { | ||
| VcfWriter.writeColumnHeader(samples, w); | ||
| wroteSamples = true; | ||
| } | ||
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| // write out record, remapping phase set if necessary | ||
| if (remapPhaseSet) { | ||
| Map<String, VcfGenotype> genotypes = new HashMap<String, VcfGenotype>(record.getGenotypes().size()); | ||
| for (Map.Entry<String, VcfGenotype> entry : record.getGenotypes().entrySet()) { | ||
| String sampleId = entry.getKey(); | ||
| VcfGenotype genotype = entry.getValue(); | ||
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||
| if (genotype.containsFieldKey("PS")) { | ||
| String oldPhaseSetId = genotype.getFieldString("PS"); | ||
| if (!phaseSetIds.containsKey(oldPhaseSetId)) { | ||
| phaseSetIds.put(oldPhaseSetId, phaseSetId); | ||
| phaseSetId++; | ||
| } | ||
| Integer newPhaseSetId = phaseSetIds.get(oldPhaseSetId); | ||
| genotypes.put(sampleId, VcfGenotype.builder(genotype).replaceField("PS", newPhaseSetId.toString()).build()); | ||
| } | ||
| else { | ||
| genotypes.put(sampleId, genotype); | ||
| } | ||
| } | ||
| VcfWriter.writeRecord(samples, VcfRecord.builder(record).replaceGenotypes(genotypes).build(), w); | ||
| } | ||
| else { | ||
| VcfWriter.writeRecord(samples, record, w); | ||
| } | ||
| } | ||
| }); | ||
|
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||
| return 0; | ||
| } | ||
| finally { | ||
| try { | ||
| writer.close(); | ||
| } | ||
| catch (Exception e) { | ||
| // empty | ||
| } | ||
| } | ||
| } | ||
|
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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"); | ||
| FileArgument inputVcfFile = new FileArgument("i", "input-vcf-file", "input VCF file, default stdin", false); | ||
| FileArgument outputVcfFile = new FileArgument("o", "output-vcf-file", "output VCF file, default stdout", false); | ||
|
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| ArgumentList arguments = new ArgumentList(about, help, inputVcfFile, outputVcfFile); | ||
| CommandLine commandLine = new CommandLine(args); | ||
|
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| RemapPhaseSet remapPhaseSet = 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); | ||
| } | ||
| remapPhaseSet = new RemapPhaseSet(inputVcfFile.getValue(), outputVcfFile.getValue()); | ||
| } | ||
| catch (CommandLineParseException e) { | ||
| if (about.wasFound()) { | ||
| About.about(System.out); | ||
| System.exit(0); | ||
| } | ||
| if (help.wasFound()) { | ||
| Usage.usage(USAGE, null, commandLine, arguments, System.out); | ||
| System.exit(0); | ||
| } | ||
| Usage.usage(USAGE, e, commandLine, arguments, System.err); | ||
| System.exit(-1); | ||
| } | ||
| catch (NullPointerException | IllegalArgumentException e) { | ||
| Usage.usage(USAGE, e, commandLine, arguments, System.err); | ||
| System.exit(-1); | ||
| } | ||
| try { | ||
| System.exit(remapPhaseSet.call()); | ||
| } | ||
| catch (Exception e) { | ||
| e.printStackTrace(); | ||
| System.exit(1); | ||
| } | ||
| } | ||
| } |
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52 changes: 52 additions & 0 deletions
52
tools/src/test/java/org/dishevelled/bio/tools/RemapPhaseSetTest.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,52 @@ | ||
| /* | ||
| dsh-bio-tools Command line tools. | ||
| Copyright (c) 2013-2017 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.junit.Assert.assertNotNull; | ||
|
|
||
| import java.io.File; | ||
|
|
||
| import org.junit.Before; | ||
| import org.junit.Test; | ||
|
|
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| /** | ||
| * Unit test for RemapPhaseSet. | ||
| * | ||
| * @author Michael Heuer | ||
| */ | ||
| public final class RemapPhaseSetTest { | ||
| private File inputVcfFile; | ||
| private File outputVcfFile; | ||
| private RemapPhaseSet remapPhaseSet; | ||
|
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| @Before | ||
| public void setUp() throws Exception { | ||
| remapPhaseSet = new RemapPhaseSet(inputVcfFile, outputVcfFile); | ||
| } | ||
|
|
||
| @Test | ||
| public void testConstructor() { | ||
| assertNotNull(remapPhaseSet); | ||
| } | ||
| } |
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