X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentUtils.java;h=f1084a7d74e40b05120a189540077ee1fddc29d0;hb=947109cebef3e98693ffc0a70b5bffcbd32217e2;hp=9278361cb2db6c854fae5306e609a83842831712;hpb=69e31ca63b3c69a4cc654df022b771b8d0bf1025;p=jalview.git diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java index 9278361..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 @@ -465,7 +468,7 @@ public class AlignmentUtils { String lastCodon = String.valueOf(cdnaSeqChars, cdnaLength - CODON_LENGTH, CODON_LENGTH).toUpperCase(); - for (String stop : ResidueProperties.STOP) + for (String stop : ResidueProperties.STOP_CODONS) { if (lastCodon.equals(stop)) { @@ -536,7 +539,8 @@ public class AlignmentUtils * allow * in protein to match untranslatable in dna */ final char aaRes = aaSeqChars[aaPos]; - if ((translated == null || "STOP".equals(translated)) && aaRes == '*') + if ((translated == null || ResidueProperties.STOP.equals(translated)) + && aaRes == '*') { continue; } @@ -568,7 +572,8 @@ public class AlignmentUtils if (dnaPos == cdnaSeqChars.length - CODON_LENGTH) { String codon = String.valueOf(cdnaSeqChars, dnaPos, CODON_LENGTH); - if ("STOP".equals(ResidueProperties.codonTranslate(codon))) + if (ResidueProperties.STOP + .equals(ResidueProperties.codonTranslate(codon))) { return true; } @@ -1102,7 +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); @@ -1886,7 +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, @@ -1911,7 +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; + } } /* @@ -1922,7 +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 @@ -1936,10 +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()) @@ -2054,9 +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()) @@ -2233,12 +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(); @@ -2410,7 +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; @@ -2428,10 +2447,17 @@ public class AlignmentUtils { for (String base : alleles.split(",")) { - String codon = base + base2 + base3; - if (addPeptideVariant(peptide, peptidePos, residue, var, codon)) + if (!base1.equalsIgnoreCase(base)) { - count++; + String codon = base.toUpperCase() + base2.toLowerCase() + + base3.toLowerCase(); + String canonical = base1.toUpperCase() + base2.toLowerCase() + + base3.toLowerCase(); + if (addPeptideVariant(peptide, peptidePos, residue, var, + codon, canonical)) + { + count++; + } } } } @@ -2450,10 +2476,17 @@ public class AlignmentUtils { for (String base : alleles.split(",")) { - String codon = base1 + base + base3; - if (addPeptideVariant(peptide, peptidePos, residue, var, codon)) + if (!base2.equalsIgnoreCase(base)) { - count++; + String codon = base1.toLowerCase() + base.toUpperCase() + + base3.toLowerCase(); + String canonical = base1.toLowerCase() + base2.toUpperCase() + + base3.toLowerCase(); + if (addPeptideVariant(peptide, peptidePos, residue, var, + codon, canonical)) + { + count++; + } } } } @@ -2472,10 +2505,17 @@ public class AlignmentUtils { for (String base : alleles.split(",")) { - String codon = base1 + base2 + base; - if (addPeptideVariant(peptide, peptidePos, residue, var, codon)) + if (!base3.equalsIgnoreCase(base)) { - count++; + String codon = base1.toLowerCase() + base2.toLowerCase() + + base.toUpperCase(); + String canonical = base1.toLowerCase() + base2.toLowerCase() + + base3.toUpperCase(); + if (addPeptideVariant(peptide, peptidePos, residue, var, + codon, canonical)) + { + count++; + } } } } @@ -2486,20 +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 @@ -2507,57 +2549,71 @@ public class AlignmentUtils * e.g. multibase variants or HGMD_MUTATION etc * are currently ignored here */ - String trans = codon.contains("-") ? "-" + String trans = codon.contains("-") ? null : (codon.length() > CODON_LENGTH ? null : ResidueProperties.codonTranslate(codon)); - if (trans != null && !trans.equals(residue)) + if (trans == null) + { + return false; + } + String desc = canonical + "/" + codon; + String featureType = ""; + if (trans.equals(residue)) + { + featureType = SequenceOntologyI.SYNONYMOUS_VARIANT; + } + else if (ResidueProperties.STOP.equals(trans)) + { + featureType = SequenceOntologyI.STOP_GAINED; + } + else { String residue3Char = StringUtils .toSentenceCase(ResidueProperties.aa2Triplet.get(residue)); String trans3Char = StringUtils .toSentenceCase(ResidueProperties.aa2Triplet.get(trans)); - String desc = "p." + residue3Char + peptidePos + trans3Char; - SequenceFeature sf = new SequenceFeature( - SequenceOntologyI.SEQUENCE_VARIANT, desc, peptidePos, - peptidePos, var.getSource()); - StringBuilder attributes = new StringBuilder(32); - String id = (String) var.variant.getValue(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); - // TODO handle other species variants JAL-2064 - StringBuilder link = new StringBuilder(32); - try - { - link.append(desc).append(" ").append(id).append( - "|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=") - .append(URLEncoder.encode(id, "UTF-8")); - sf.addLink(link.toString()); - } catch (UnsupportedEncodingException e) - { - // as if - } - } - String clinSig = (String) var.variant.getValue(CLINICAL_SIGNIFICANCE); - if (clinSig != null) + desc = "p." + residue3Char + peptidePos + trans3Char; + featureType = SequenceOntologyI.NONSYNONYMOUS_VARIANT; + } + SequenceFeature sf = new SequenceFeature(featureType, desc, peptidePos, + peptidePos, var.getSource()); + + StringBuilder attributes = new StringBuilder(32); + String id = (String) var.variant.getValue(VARIANT_ID); + if (id != null) + { + if (id.startsWith(SEQUENCE_VARIANT)) { - sf.setValue(CLINICAL_SIGNIFICANCE, clinSig); - attributes.append(";").append(CLINICAL_SIGNIFICANCE).append("=") - .append(clinSig); + id = id.substring(SEQUENCE_VARIANT.length()); } - peptide.addSequenceFeature(sf); - if (attributes.length() > 0) + 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 + { + link.append(desc).append(" ").append(id).append( + "|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=") + .append(URLEncoder.encode(id, "UTF-8")); + sf.addLink(link.toString()); + } catch (UnsupportedEncodingException e) { - sf.setAttributes(attributes.toString()); + // as if } - return true; } - return false; + String clinSig = (String) var.variant.getValue(CLINICAL_SIGNIFICANCE); + if (clinSig != null) + { + sf.setValue(CLINICAL_SIGNIFICANCE, clinSig); + attributes.append(";").append(CLINICAL_SIGNIFICANCE).append("=") + .append(clinSig); + } + peptide.addSequenceFeature(sf); + if (attributes.length() > 0) + { + sf.setAttributes(attributes.toString()); + } + return true; } /**