use of com.milaboratory.core.sequence.AminoAcidSequence in project repseqio by repseqio.
the class DebugAction method getAminoAcidSequence.
private static AminoAcidSequence getAminoAcidSequence(VDJCGene gene, GeneFeature geneFeature, NucleotideSequence nSequence) {
ReferencePoints partitioning = gene.getPartitioning();
ReferencePoint frameReference = GeneFeature.getFrameReference(geneFeature);
AminoAcidSequence aaSequence;
if (frameReference != null) {
int relativePosition = partitioning.getRelativePosition(geneFeature, frameReference);
aaSequence = nSequence == null || relativePosition < 0 ? null : AminoAcidSequence.translate(nSequence, withIncompleteCodon(relativePosition));
} else
aaSequence = null;
return aaSequence;
}
use of com.milaboratory.core.sequence.AminoAcidSequence in project repseqio by repseqio.
the class FromFastaActionAbstract method go.
@Override
public void go(ActionHelper helper) throws Exception {
Pattern functionalityRegexp = params.getFunctionalityRegexp();
GeneType geneType = params.getGeneType();
Map<String, VDJCGeneData> genes = new HashMap<>();
Path libraryPath = Paths.get(params.getOutputJSON()).toAbsolutePath();
// Parsing -P or --gene-feature parameters
Map<ReferencePoint, Integer> points = new HashMap<>();
if (params.geneFeature != null) {
GeneFeature gf = params.getGeneFeature();
points.put(gf.getFirstPoint(), 0);
points.put(gf.getLastPoint(), -1);
} else
for (Map.Entry<String, String> p : params.points.entrySet()) {
ReferencePoint anchorPoint = ReferencePoint.getPointByName(p.getKey());
if (anchorPoint == null)
throw new IllegalArgumentException("Unknown anchor point: " + p.getKey());
int position = Integer.decode(p.getValue());
points.put(anchorPoint, position);
}
// Check
for (Map.Entry<ReferencePoint, Integer> entry : points.entrySet()) if (entry.getKey().getGeneType() != null && entry.getKey().getGeneType() != geneType)
throw new IllegalArgumentException("Incompatible anchor point and gene type: " + entry.getKey() + " / " + geneType);
try (FastaReader reader = new FastaReader<>(params.getInput(), null);
SequenceStorage storage = params.doEmbedSequences() ? new EmbeddedWriter() : params.getOutputFasta() == null ? new ExistingFileWriter(libraryPath, Paths.get(params.getInput()).toAbsolutePath()) : new FastaSequenceStorage(libraryPath, Paths.get(params.getOutputFasta()).toAbsolutePath())) {
for (FastaReader.RawFastaRecord record : CUtils.it((OutputPortCloseable<FastaReader.RawFastaRecord>) reader.asRawRecordsPort())) {
StringWithMapping swm = StringWithMapping.removeSymbol(record.sequence, params.getPaddingCharacter());
NucleotideSequence seq = new NucleotideSequence(swm.getModifiedString());
if (seq.containsWildcards()) {
System.out.println("Sequence dropped because contain wildcards: " + record.description);
continue;
}
String[] fields = record.description.split("\\|");
String geneName = fields[params.nameIndex];
boolean functionality = true;
if (params.functionalityIndex != null)
functionality = functionalityRegexp.matcher(fields[params.functionalityIndex]).matches();
SortedMap<ReferencePoint, Long> anchorPoints = new TreeMap<>();
for (Map.Entry<String, String> p : params.patterns.entrySet()) {
ReferencePoint anchorPoint = ReferencePoint.getPointByName(p.getKey());
if (anchorPoint == null)
throw new IllegalArgumentException("Unknown anchor point: " + p.getKey());
if (anchorPoint.getGeneType() != null && anchorPoint.getGeneType() != geneType)
throw new IllegalArgumentException("Incompatible anchor point and gene type: " + anchorPoint + " / " + geneType);
Pattern pattern = Pattern.compile(p.getValue());
int position = -1;
for (boolean stops : new boolean[] { false, true }) for (int f = 0; f < 3; f++) {
if (position != -1)
continue;
TranslationParameters tp = TranslationParameters.withoutIncompleteCodon(f);
AminoAcidSequence aa = AminoAcidSequence.translate(seq, tp);
if (!stops && aa.containStops())
continue;
String str = aa.toString();
Matcher matcher = pattern.matcher(str);
if (matcher.find()) {
int aaPosition = matcher.start(1);
position = AminoAcidSequence.convertAAPositionToNt(aaPosition, seq.size(), tp);
}
}
if (position == -1)
continue;
anchorPoints.put(anchorPoint, (long) position);
}
for (Map.Entry<ReferencePoint, Integer> p : points.entrySet()) {
// AA patterns have priority over positional anchor points
if (anchorPoints.containsKey(p.getKey()))
continue;
// Converting position using
int position = swm.convertPosition(p.getValue());
// Can't be converted (e.g. position of padding symbol) skipping
if (position == -1)
continue;
anchorPoints.put(p.getKey(), (long) position);
}
if (genes.containsKey(geneName)) {
if (params.getIgnoreDuplicates()) {
System.out.println("Ignored: Duplicate records for " + geneName);
continue;
} else
throw new IllegalArgumentException("Duplicate records for " + geneName);
}
BaseSequence baseSequence = storage.storeSequence(seq, geneName, record.description);
VDJCGeneData gene = new VDJCGeneData(baseSequence, geneName, geneType, functionality, new Chains(params.chain), new TreeMap<String, SortedSet<String>>(), anchorPoints).addMetaValue(KnownVDJCGeneMetaFields.COMMENTS, record.description);
genes.put(geneName, gene);
}
VDJCLibraryData library = new VDJCLibraryData(params.taxonId, params.speciesNames, new ArrayList<>(genes.values()), new TreeMap<String, SortedSet<String>>(), storage.getBase()).addMetaValue(KnownVDJCLibraryMetaFields.COMMENTS, "Imported from: " + params.getInput());
VDJCDataUtils.writeToFile(new VDJCLibraryData[] { library }, params.getOutputJSON(), false);
}
}
use of com.milaboratory.core.sequence.AminoAcidSequence in project mixcr by milaboratory.
the class BackwardCompatibilityTests method assertGoodCLNS.
public static void assertGoodCLNS(String resource, int size, int good, double sumCount) throws IOException {
CloneSet cloneSet = CloneSetIO.read(BackwardCompatibilityTests.class.getResource(resource).getFile());
Assert.assertEquals(size, cloneSet.size());
int countGood = 0;
for (Clone clone : cloneSet.getClones()) {
sumCount -= clone.getCount();
AminoAcidSequence aaCDR3 = AminoAcidSequence.translateFromCenter(clone.getFeature(GeneFeature.CDR3).getSequence());
if (aaCDR3.codeAt(0) == AminoAcidAlphabet.C && aaCDR3.codeAt(aaCDR3.size() - 1) == AminoAcidAlphabet.F) {
++countGood;
}
}
Assert.assertEquals(0, sumCount, 0.01);
Assert.assertEquals(good, countGood);
}
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