X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentUtils.java;h=f1084a7d74e40b05120a189540077ee1fddc29d0;hb=947109cebef3e98693ffc0a70b5bffcbd32217e2;hp=bdc5fc16373ad8465ac7d3611ad0d1b04844bdd3;hpb=6a99631de459c9ba52894900d08be0a2d6500488;p=jalview.git diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java index bdc5fc1..f1084a7 100644 --- a/src/jalview/analysis/AlignmentUtils.java +++ b/src/jalview/analysis/AlignmentUtils.java @@ -24,7 +24,6 @@ import static jalview.io.gff.GffConstants.CLINICAL_SIGNIFICANCE; import jalview.datamodel.AlignedCodon; import jalview.datamodel.AlignedCodonFrame; -import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; @@ -36,6 +35,7 @@ import jalview.datamodel.Sequence; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; +import jalview.datamodel.SequenceMapping; import jalview.datamodel.features.SequenceFeatures; import jalview.io.gff.Gff3Helper; import jalview.io.gff.SequenceOntologyI; @@ -74,12 +74,15 @@ import java.util.TreeMap; */ public class AlignmentUtils { - private static final int CODON_LENGTH = 3; private static final String SEQUENCE_VARIANT = "sequence_variant:"; - private static final String ID = "ID"; + /* + * the 'id' attribute is provided for variant features fetched from + * Ensembl using its REST service with JSON format + */ + public static final String VARIANT_ID = "id"; /** * A data model to hold the 'normal' base value at a position, and an optional @@ -1104,7 +1107,7 @@ public class AlignmentUtils SequenceI prot = mapping.findAlignedSequence(dnaSeq, protein); if (prot != null) { - Mapping seqMap = mapping.getMappingForSequence(dnaSeq); + Mapping seqMap = mapping.getMappingForSequence(dnaSeq, false); addCodonPositions(dnaSeq, prot, protein.getGapCharacter(), seqMap, alignedCodons); unmappedProtein.remove(prot); @@ -1888,7 +1891,7 @@ public class AlignmentUtils * @param seqMappings * the set of mappings involving dnaSeq * @param aMapping - * an initial candidate from seqMappings + * a transcript-to-peptide mapping * @return */ static SequenceI findCdsForProtein(List mappings, @@ -1913,7 +1916,15 @@ public class AlignmentUtils if (mappedFromLength == dnaLength || mappedFromLength == dnaLength - CODON_LENGTH) { - return seqDss; + /* + * if sequence has CDS features, this is a transcript with no UTR + * - do not take this as the CDS sequence! (JAL-2789) + */ + if (seqDss.getFeatures().getFeaturesByOntology(SequenceOntologyI.CDS) + .isEmpty()) + { + return seqDss; + } } /* @@ -1924,7 +1935,7 @@ public class AlignmentUtils .findMappingsForSequence(proteinProduct, mappings); for (AlignedCodonFrame acf : mappingsToPeptide) { - for (SequenceToSequenceMapping map : acf.getMappings()) + for (SequenceMapping map : acf.getMappings()) { Mapping mapping = map.getMapping(); if (mapping != aMapping @@ -1938,10 +1949,12 @@ public class AlignmentUtils { /* * found a 3:1 mapping to the protein product which covers - * the whole dna sequence i.e. is from CDS; finally check it - * is from the dna start sequence + * the whole dna sequence i.e. is from CDS; finally check the CDS + * is mapped from the given dna start sequence */ SequenceI cdsSeq = map.getFromSeq(); + // todo this test is weak if seqMappings contains multiple mappings; + // we get away with it if transcript:cds relationship is 1:1 List dnaToCdsMaps = MappingUtils .findMappingsForSequence(cdsSeq, seqMappings); if (!dnaToCdsMaps.isEmpty()) @@ -2056,9 +2069,11 @@ public class AlignmentUtils protected static List propagateDBRefsToCDS(SequenceI cdsSeq, SequenceI contig, SequenceI proteinProduct, Mapping mapping) { + // gather direct refs from contig congruent with mapping List direct = new ArrayList<>(); HashSet directSources = new HashSet<>(); + if (contig.getDBRefs() != null) { for (DBRefEntry dbr : contig.getDBRefs()) @@ -2235,12 +2250,13 @@ public class AlignmentUtils int mappedDnaLength = MappingUtils.getLength(ranges); /* - * if not a whole number of codons, something is wrong, - * abort mapping + * if not a whole number of codons, truncate mapping */ - if (mappedDnaLength % CODON_LENGTH > 0) + int codonRemainder = mappedDnaLength % CODON_LENGTH; + if (codonRemainder > 0) { - return null; + mappedDnaLength -= codonRemainder; + MappingUtils.removeEndPositions(codonRemainder, ranges); } int proteinLength = proteinSeq.getLength(); @@ -2412,7 +2428,8 @@ public class AlignmentUtils static int computePeptideVariants(SequenceI peptide, int peptidePos, List[] codonVariants) { - String residue = String.valueOf(peptide.getCharAt(peptidePos - 1)); + 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; @@ -2430,11 +2447,14 @@ public class AlignmentUtils { for (String base : alleles.split(",")) { - if (!base1.equals(base)) + if (!base1.equalsIgnoreCase(base)) { - String codon = base + base2 + base3; + String codon = base.toUpperCase() + base2.toLowerCase() + + base3.toLowerCase(); + String canonical = base1.toUpperCase() + base2.toLowerCase() + + base3.toLowerCase(); if (addPeptideVariant(peptide, peptidePos, residue, var, - codon)) + codon, canonical)) { count++; } @@ -2456,11 +2476,14 @@ public class AlignmentUtils { for (String base : alleles.split(",")) { - if (!base2.equals(base)) + if (!base2.equalsIgnoreCase(base)) { - String codon = base1 + base + base3; + String codon = base1.toLowerCase() + base.toUpperCase() + + base3.toLowerCase(); + String canonical = base1.toLowerCase() + base2.toUpperCase() + + base3.toLowerCase(); if (addPeptideVariant(peptide, peptidePos, residue, var, - codon)) + codon, canonical)) { count++; } @@ -2482,11 +2505,14 @@ public class AlignmentUtils { for (String base : alleles.split(",")) { - if (!base3.equals(base)) + if (!base3.equalsIgnoreCase(base)) { - String codon = base1 + base2 + base; + String codon = base1.toLowerCase() + base2.toLowerCase() + + base.toUpperCase(); + String canonical = base1.toLowerCase() + base2.toLowerCase() + + base3.toUpperCase(); if (addPeptideVariant(peptide, peptidePos, residue, var, - codon)) + codon, canonical)) { count++; } @@ -2500,20 +2526,22 @@ public class AlignmentUtils } /** - * Helper method that adds a peptide variant feature, provided the given codon - * translates to a value different to the current residue (is a non-synonymous - * variant). ID and clinical_significance attributes of the dna variant (if - * present) are copied to the new feature. + * Helper method that adds a peptide variant feature. ID and + * clinical_significance attributes of the dna variant (if present) are copied + * to the new feature. * * @param peptide * @param peptidePos * @param residue * @param var * @param codon + * the variant codon e.g. aCg + * @param canonical + * the 'normal' codon e.g. aTg * @return true if a feature was added, else false */ static boolean addPeptideVariant(SequenceI peptide, int peptidePos, - String residue, DnaVariant var, String codon) + String residue, DnaVariant var, String codon, String canonical) { /* * get peptide translation of codon e.g. GAT -> D @@ -2528,7 +2556,7 @@ public class AlignmentUtils { return false; } - String desc = codon; + String desc = canonical + "/" + codon; String featureType = ""; if (trans.equals(residue)) { @@ -2551,15 +2579,15 @@ public class AlignmentUtils peptidePos, var.getSource()); StringBuilder attributes = new StringBuilder(32); - String id = (String) var.variant.getValue(ID); + String id = (String) var.variant.getValue(VARIANT_ID); if (id != null) { if (id.startsWith(SEQUENCE_VARIANT)) { id = id.substring(SEQUENCE_VARIANT.length()); } - sf.setValue(ID, id); - attributes.append(ID).append("=").append(id); + sf.setValue(VARIANT_ID, id); + attributes.append(VARIANT_ID).append("=").append(id); // TODO handle other species variants JAL-2064 StringBuilder link = new StringBuilder(32); try