+ /*
+ * start of exon is in CDS range - 3' overlap
+ * to a range up to the end of the peptide
+ */
+ mappedTo[1] = toSeq.getLength();
+ }
+ }
+ if (mappedTo != null)
+ {
+ int newBegin = Math.min(mappedTo[0], mappedTo[1]);
+ int newEnd = Math.max(mappedTo[0], mappedTo[1]);
+ SequenceFeature copy = new SequenceFeature(sf, newBegin, newEnd,
+ sf.getFeatureGroup(), sf.getScore());
+ copyTo.addSequenceFeature(copy);
+ count++;
+ }
+ }
+ return count;
+ }
+
+ /**
+ * Returns a mapping from dna to protein by inspecting sequence features of
+ * type "CDS" on the dna. A mapping is constructed if the total CDS feature
+ * length is 3 times the peptide length (optionally after dropping a trailing
+ * stop codon). This method does not check whether the CDS nucleotide sequence
+ * translates to the peptide sequence.
+ *
+ * @param dnaSeq
+ * @param proteinSeq
+ * @return
+ */
+ public static MapList mapCdsToProtein(SequenceI dnaSeq,
+ SequenceI proteinSeq)
+ {
+ List<int[]> ranges = findCdsPositions(dnaSeq);
+ int mappedDnaLength = MappingUtils.getLength(ranges);
+
+ /*
+ * if not a whole number of codons, truncate mapping
+ */
+ int codonRemainder = mappedDnaLength % CODON_LENGTH;
+ if (codonRemainder > 0)
+ {
+ mappedDnaLength -= codonRemainder;
+ MappingUtils.removeEndPositions(codonRemainder, ranges);
+ }
+
+ int proteinLength = proteinSeq.getLength();
+ int proteinStart = proteinSeq.getStart();
+ int proteinEnd = proteinSeq.getEnd();
+
+ /*
+ * incomplete start codon may mean X at start of peptide
+ * we ignore both for mapping purposes
+ */
+ if (proteinSeq.getCharAt(0) == 'X')
+ {
+ // todo JAL-2022 support startPhase > 0
+ proteinStart++;
+ proteinLength--;
+ }
+ List<int[]> proteinRange = new ArrayList<>();
+
+ /*
+ * dna length should map to protein (or protein plus stop codon)
+ */
+ int codesForResidues = mappedDnaLength / CODON_LENGTH;
+ if (codesForResidues == (proteinLength + 1))
+ {
+ // assuming extra codon is for STOP and not in peptide
+ // todo: check trailing codon is indeed a STOP codon
+ codesForResidues--;
+ mappedDnaLength -= CODON_LENGTH;
+ MappingUtils.removeEndPositions(CODON_LENGTH, ranges);
+ }
+
+ if (codesForResidues == proteinLength)
+ {
+ proteinRange.add(new int[] { proteinStart, proteinEnd });
+ return new MapList(ranges, proteinRange, CODON_LENGTH, 1);
+ }
+ return null;
+ }
+
+ /**
+ * Returns a list of CDS ranges found (as sequence positions base 1), i.e. of
+ * [start, end] positions of sequence features of type "CDS" (or a sub-type of
+ * CDS in the Sequence Ontology). The ranges are sorted into ascending start
+ * position order, so this method is only valid for linear CDS in the same
+ * sense as the protein product.
+ *
+ * @param dnaSeq
+ * @return
+ */
+ protected static List<int[]> findCdsPositions(SequenceI dnaSeq)
+ {
+ List<int[]> result = new ArrayList<>();
+
+ List<SequenceFeature> sfs = dnaSeq.getFeatures().getFeaturesByOntology(
+ SequenceOntologyI.CDS);
+ if (sfs.isEmpty())
+ {
+ return result;
+ }
+ SequenceFeatures.sortFeatures(sfs, true);
+
+ for (SequenceFeature sf : sfs)
+ {
+ int phase = 0;
+ try
+ {
+ phase = Integer.parseInt(sf.getPhase());
+ } catch (NumberFormatException e)
+ {
+ // ignore
+ }
+ /*
+ * phase > 0 on first codon means 5' incomplete - skip to the start
+ * of the next codon; example ENST00000496384
+ */
+ int begin = sf.getBegin();
+ int end = sf.getEnd();
+ if (result.isEmpty() && phase > 0)
+ {
+ begin += phase;
+ if (begin > end)
+ {
+ // shouldn't happen!
+ System.err
+ .println("Error: start phase extends beyond start CDS in "
+ + dnaSeq.getName());
+ }
+ }
+ result.add(new int[] { begin, end });
+ }
+
+ /*
+ * Finally sort ranges by start position. This avoids a dependency on
+ * keeping features in order on the sequence (if they are in order anyway,
+ * the sort will have almost no work to do). The implicit assumption is CDS
+ * ranges are assembled in order. Other cases should not use this method,
+ * but instead construct an explicit mapping for CDS (e.g. EMBL parsing).
+ */
+ Collections.sort(result, IntRangeComparator.ASCENDING);
+ return result;
+ }
+
+ /**
+ * Maps exon features from dna to protein, and computes variants in peptide
+ * product generated by variants in dna, and adds them as sequence_variant
+ * features on the protein sequence. Returns the number of variant features
+ * added.
+ *
+ * @param dnaSeq
+ * @param peptide
+ * @param dnaToProtein
+ */
+ public static int computeProteinFeatures(SequenceI dnaSeq,
+ SequenceI peptide, MapList dnaToProtein)
+ {
+ while (dnaSeq.getDatasetSequence() != null)
+ {
+ dnaSeq = dnaSeq.getDatasetSequence();
+ }
+ while (peptide.getDatasetSequence() != null)
+ {
+ peptide = peptide.getDatasetSequence();
+ }
+
+ transferFeatures(dnaSeq, peptide, dnaToProtein, SequenceOntologyI.EXON);
+
+ /*
+ * compute protein variants from dna variants and codon mappings;
+ * NB - alternatively we could retrieve this using the REST service e.g.
+ * http://rest.ensembl.org/overlap/translation
+ * /ENSP00000288602?feature=transcript_variation;content-type=text/xml
+ * which would be a bit slower but possibly more reliable
+ */
+
+ /*
+ * build a map with codon variations for each potentially varying peptide
+ */
+ LinkedHashMap<Integer, List<DnaVariant>[]> variants = buildDnaVariantsMap(
+ dnaSeq, dnaToProtein);
+
+ /*
+ * scan codon variations, compute peptide variants and add to peptide sequence
+ */
+ int count = 0;
+ for (Entry<Integer, List<DnaVariant>[]> variant : variants.entrySet())
+ {
+ int peptidePos = variant.getKey();
+ List<DnaVariant>[] codonVariants = variant.getValue();
+ count += computePeptideVariants(peptide, peptidePos, codonVariants);
+ }
+
+ return count;
+ }
+
+ /**
+ * Computes non-synonymous peptide variants from codon variants and adds them
+ * as sequence_variant features on the protein sequence (one feature per
+ * allele variant). Selected attributes (variant id, clinical significance)
+ * are copied over to the new features.
+ *
+ * @param peptide
+ * the protein sequence
+ * @param peptidePos
+ * the position to compute peptide variants for
+ * @param codonVariants
+ * a list of dna variants per codon position
+ * @return the number of features added
+ */
+ static int computePeptideVariants(SequenceI peptide, int peptidePos,
+ List<DnaVariant>[] codonVariants)
+ {
+ String residue = String
+ .valueOf(peptide.getCharAt(peptidePos - peptide.getStart()));
+ int count = 0;
+ String base1 = codonVariants[0].get(0).base;
+ String base2 = codonVariants[1].get(0).base;
+ String base3 = codonVariants[2].get(0).base;
+
+ /*
+ * variants in first codon base
+ */
+ for (DnaVariant var : codonVariants[0])
+ {
+ if (var.variant != null)
+ {
+ String alleles = (String) var.variant.getValue(Gff3Helper.ALLELES);
+ if (alleles != null)
+ {
+ for (String base : alleles.split(","))