-
Notifications
You must be signed in to change notification settings - Fork 78
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
1 parent
843bcd6
commit f2f1f1d
Showing
8 changed files
with
284 additions
and
31 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,3 +1,5 @@ | ||
| Added export options -vHitsWithoutScores (same for J and D genes) | ||
|
|
||
| Added compression for .vdjca and .clns files (when specifying additional ".gz" extension: e.g. "mixcr align inut.fastq output.vdjca.gz" etc.) | ||
| Added compression for .vdjca and .clns files (when specifying additional ".gz" extension: e.g. "mixcr align inut.fastq output.vdjca.gz" etc.) | ||
|
|
||
| Fixed #6 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
194 changes: 194 additions & 0 deletions
194
src/main/java/com/milaboratory/mixcr/util/RunMiXCR.java
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,194 @@ | ||
| package com.milaboratory.mixcr.util; | ||
|
|
||
| import cc.redberry.pipe.CUtils; | ||
| import cc.redberry.pipe.OutputPort; | ||
| import cc.redberry.pipe.OutputPortCloseable; | ||
| import cc.redberry.pipe.blocks.ParallelProcessor; | ||
| import cc.redberry.pipe.util.Chunk; | ||
| import cc.redberry.pipe.util.Indexer; | ||
| import cc.redberry.pipe.util.OrderedOutputPort; | ||
| import com.milaboratory.core.io.sequence.SequenceRead; | ||
| import com.milaboratory.core.io.sequence.SequenceReaderCloseable; | ||
| import com.milaboratory.core.io.sequence.fasta.FastaReader; | ||
| import com.milaboratory.core.io.sequence.fasta.FastaSequenceReaderWrapper; | ||
| import com.milaboratory.core.io.sequence.fastq.PairedFastqReader; | ||
| import com.milaboratory.core.io.sequence.fastq.SingleFastqReader; | ||
| import com.milaboratory.core.sequence.NucleotideSequence; | ||
| import com.milaboratory.mixcr.assembler.*; | ||
| import com.milaboratory.mixcr.basictypes.CloneSet; | ||
| import com.milaboratory.mixcr.basictypes.VDJCAlignments; | ||
| import com.milaboratory.mixcr.cli.AlignerReport; | ||
| import com.milaboratory.mixcr.cli.CloneAssemblerReport; | ||
| import com.milaboratory.mixcr.reference.*; | ||
| import com.milaboratory.mixcr.vdjaligners.VDJCAligner; | ||
| import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters; | ||
| import com.milaboratory.mixcr.vdjaligners.VDJCAlignmentResult; | ||
| import com.milaboratory.mixcr.vdjaligners.VDJCParametersPresets; | ||
| import com.milaboratory.util.CanReportProgress; | ||
| import com.milaboratory.util.SmartProgressReporter; | ||
|
|
||
| import java.io.IOException; | ||
| import java.util.ArrayList; | ||
| import java.util.EnumSet; | ||
| import java.util.List; | ||
| import java.util.Set; | ||
|
|
||
| import static cc.redberry.pipe.CUtils.chunked; | ||
| import static cc.redberry.pipe.CUtils.unchunked; | ||
|
|
||
| /** | ||
| * @author Dmitry Bolotin | ||
| * @author Stanislav Poslavsky | ||
| */ | ||
| public final class RunMiXCR { | ||
|
|
||
| public static AssembleResult assemble(final AlignResult align) { | ||
| RunMiXCRAnalysis parameters = align.parameters; | ||
| try (CloneAssembler assembler = new CloneAssembler(parameters.cloneAssemblerParameters, | ||
| false, align.usedAlleles)) { | ||
|
|
||
| CloneAssemblerReport report = new CloneAssemblerReport(); | ||
| assembler.setListener(report); | ||
|
|
||
| CloneAssemblerRunner assemblerRunner = new CloneAssemblerRunner(new AlignmentsProvider() { | ||
| @Override | ||
| public OutputPortCloseable<VDJCAlignments> create() { | ||
| return opCloseable(CUtils.asOutputPort(align.alignments)); | ||
| } | ||
|
|
||
| @Override | ||
| public long getTotalNumberOfReads() { | ||
| return align.alignments.size(); | ||
| } | ||
| }, assembler, parameters.threads); | ||
|
|
||
| //start progress reporting | ||
| SmartProgressReporter.startProgressReport(assemblerRunner); | ||
|
|
||
| assemblerRunner.run(); | ||
|
|
||
| CloneSet cloneSet = assemblerRunner.getCloneSet(); | ||
| return new AssembleResult(cloneSet, report); | ||
| } | ||
| } | ||
|
|
||
| public static AlignResult align(String... files) throws Exception { | ||
| return align(new RunMiXCRAnalysis(files)); | ||
| } | ||
|
|
||
| public static AlignResult align(RunMiXCRAnalysis parameters) throws Exception { | ||
| VDJCAlignerParameters alignerParameters = parameters.alignerParameters; | ||
|
|
||
| VDJCAligner aligner = VDJCAligner.createAligner(alignerParameters, | ||
| parameters.isInputPaired(), alignerParameters.getMergerParameters() != null); | ||
|
|
||
| LociLibrary ll = LociLibraryManager.getDefault().getLibrary("mi"); | ||
|
|
||
| List<Allele> alleles = new ArrayList<>(); | ||
| for (Locus locus : parameters.loci) | ||
| for (Allele allele : ll.getLocus(parameters.taxonId, locus).getAllAlleles()) | ||
| if (alignerParameters.containsRequiredFeature(allele) && | ||
| (allele.isFunctional() || !parameters.isFunctionalOnly)) { | ||
| alleles.add(allele); | ||
| aligner.addAllele(allele); | ||
| } | ||
|
|
||
| AlignerReport report = new AlignerReport(); | ||
| aligner.setEventsListener(report); | ||
|
|
||
| try (SequenceReaderCloseable<? extends SequenceRead> reader = parameters.createReader()) { | ||
|
|
||
| //start progress reporting | ||
| SmartProgressReporter.startProgressReport("align", (CanReportProgress) reader); | ||
|
|
||
| OutputPort<Chunk<SequenceRead>> mainInputReads = CUtils.buffered((OutputPort) chunked(reader, 64), 16); | ||
| OutputPort<VDJCAlignmentResult> alignments = unchunked(new ParallelProcessor(mainInputReads, chunked(aligner), parameters.threads)); | ||
| List<VDJCAlignments> als = new ArrayList<>(); | ||
| int ind = 0; | ||
| for (VDJCAlignmentResult t : CUtils.it(new OrderedOutputPort<>(alignments, new Indexer<VDJCAlignmentResult>() { | ||
| @Override | ||
| public long getIndex(VDJCAlignmentResult r) { | ||
| return r.read.getId(); | ||
| } | ||
| }))) { | ||
| if (t.alignment != null) { | ||
| t.alignment.setAlignmentsIndex(ind++); | ||
| als.add(t.alignment); | ||
| } | ||
| } | ||
| return new AlignResult(parameters, reader.getNumberOfReads(), report, als, alleles); | ||
| } | ||
| } | ||
|
|
||
| public static final class AssembleResult { | ||
| final CloneSet cloneSet; | ||
| final CloneAssemblerReport report; | ||
|
|
||
| public AssembleResult(CloneSet cloneSet, CloneAssemblerReport report) { | ||
| this.cloneSet = cloneSet; | ||
| this.report = report; | ||
| } | ||
| } | ||
|
|
||
| public static final class AlignResult { | ||
| final RunMiXCRAnalysis parameters; | ||
| final long totalNumberOfReads; | ||
| final AlignerReport report; | ||
| final List<VDJCAlignments> alignments; | ||
| final List<Allele> usedAlleles; | ||
|
|
||
| public AlignResult(RunMiXCRAnalysis parameters, long totalNumberOfReads, AlignerReport report, | ||
| List<VDJCAlignments> alignments, List<Allele> usedAlleles) { | ||
| this.parameters = parameters; | ||
| this.totalNumberOfReads = totalNumberOfReads; | ||
| this.report = report; | ||
| this.alignments = alignments; | ||
| this.usedAlleles = usedAlleles; | ||
| } | ||
| } | ||
|
|
||
| public static final class RunMiXCRAnalysis { | ||
| public VDJCAlignerParameters alignerParameters = VDJCParametersPresets.getByName("default"); | ||
| public CloneAssemblerParameters cloneAssemblerParameters = CloneAssemblerParametersPresets.getByName("default"); | ||
| public Set<Locus> loci = EnumSet.allOf(Locus.class); | ||
| public int taxonId = Species.HomoSapiens; | ||
| public boolean isFunctionalOnly = true; | ||
| public int threads = Runtime.getRuntime().availableProcessors(); | ||
| public final String[] inputFiles; | ||
|
|
||
| public RunMiXCRAnalysis(String... inputFiles) { | ||
| this.inputFiles = inputFiles; | ||
| } | ||
|
|
||
| public boolean isInputPaired() { | ||
| return inputFiles.length == 2; | ||
| } | ||
|
|
||
| public SequenceReaderCloseable<? extends SequenceRead> createReader() throws IOException { | ||
| if (isInputPaired()) | ||
| return new PairedFastqReader(inputFiles[0], inputFiles[1], true); | ||
| else { | ||
| String[] s = inputFiles[0].split("\\."); | ||
| if (s[s.length - 1].equals("fasta")) | ||
| return new FastaSequenceReaderWrapper( | ||
| new FastaReader<>(inputFiles[0], NucleotideSequence.ALPHABET), | ||
| true); | ||
| else | ||
| return new SingleFastqReader(inputFiles[0], true); | ||
| } | ||
| } | ||
| } | ||
|
|
||
| private static <T> OutputPortCloseable<T> opCloseable(final OutputPort<T> op) { | ||
| return new OutputPortCloseable<T>() { | ||
| @Override | ||
| public void close() { | ||
| } | ||
|
|
||
| @Override | ||
| public T take() { | ||
| return op.take(); | ||
| } | ||
| }; | ||
| } | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.