From: Jim Procter Date: Tue, 30 Aug 2016 13:30:34 +0000 (+0100) Subject: Merge branch 'develop' into merge/develop_bug/JAL-2154projectMappings X-Git-Tag: Release_2_10_0~47^2~4^2~31 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;ds=sidebyside;h=a3b6803932b6b0ce73a44982bc58c56b7b4def4b;hp=-c;p=jalview.git Merge branch 'develop' into merge/develop_bug/JAL-2154projectMappings --- a3b6803932b6b0ce73a44982bc58c56b7b4def4b diff --combined src/jalview/analysis/AlignmentUtils.java index b0a2269,d1cd5a3..ea330d8 --- a/src/jalview/analysis/AlignmentUtils.java +++ b/src/jalview/analysis/AlignmentUtils.java @@@ -22,6 -22,7 +22,6 @@@ package jalview.analysis import static jalview.io.gff.GffConstants.CLINICAL_SIGNIFICANCE; -import jalview.api.DBRefEntryI; import jalview.datamodel.AlignedCodon; import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping; @@@ -72,6 -73,7 +72,7 @@@ 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"; @@@ -79,15 -81,16 +80,16 @@@ * A data model to hold the 'normal' base value at a position, and an optional * sequence variant feature */ - static class DnaVariant + static final class DnaVariant { - String base; + final String base; SequenceFeature variant; DnaVariant(String nuc) { base = nuc; + variant = null; } DnaVariant(String nuc, SequenceFeature var) @@@ -95,6 -98,11 +97,11 @@@ base = nuc; variant = var; } + + public String getSource() + { + return variant == null ? null : variant.getFeatureGroup(); + } } /** @@@ -427,7 -435,7 +434,7 @@@ /* * cdnaStart/End, proteinStartEnd are base 1 (for dataset sequence mapping) */ - final int mappedLength = 3 * aaSeqChars.length; + final int mappedLength = CODON_LENGTH * aaSeqChars.length; int cdnaLength = cdnaSeqChars.length; int cdnaStart = cdnaSeq.getStart(); int cdnaEnd = cdnaSeq.getEnd(); @@@ -439,14 -447,14 +446,14 @@@ */ if (cdnaLength != mappedLength && cdnaLength > 2) { - String lastCodon = String.valueOf(cdnaSeqChars, cdnaLength - 3, 3) + String lastCodon = String.valueOf(cdnaSeqChars, cdnaLength - CODON_LENGTH, CODON_LENGTH) .toUpperCase(); for (String stop : ResidueProperties.STOP) { if (lastCodon.equals(stop)) { - cdnaEnd -= 3; - cdnaLength -= 3; + cdnaEnd -= CODON_LENGTH; + cdnaLength -= CODON_LENGTH; break; } } @@@ -458,12 -466,12 +465,12 @@@ int startOffset = 0; if (cdnaLength != mappedLength && cdnaLength > 2 - && String.valueOf(cdnaSeqChars, 0, 3).toUpperCase() + && String.valueOf(cdnaSeqChars, 0, CODON_LENGTH).toUpperCase() .equals(ResidueProperties.START)) { - startOffset += 3; - cdnaStart += 3; - cdnaLength -= 3; + startOffset += CODON_LENGTH; + cdnaStart += CODON_LENGTH; + cdnaLength -= CODON_LENGTH; } if (translatesAs(cdnaSeqChars, startOffset, aaSeqChars)) @@@ -472,7 -480,7 +479,7 @@@ * protein is translation of dna (+/- start/stop codons) */ MapList map = new MapList(new int[] { cdnaStart, cdnaEnd }, new int[] - { proteinStart, proteinEnd }, 3, 1); + { proteinStart, proteinEnd }, CODON_LENGTH, 1); return map; } @@@ -503,9 -511,9 +510,9 @@@ int aaPos = 0; int dnaPos = cdnaStart; for (; dnaPos < cdnaSeqChars.length - 2 - && aaPos < aaSeqChars.length; dnaPos += 3, aaPos++) + && aaPos < aaSeqChars.length; dnaPos += CODON_LENGTH, aaPos++) { - String codon = String.valueOf(cdnaSeqChars, dnaPos, 3); + String codon = String.valueOf(cdnaSeqChars, dnaPos, CODON_LENGTH); final String translated = ResidueProperties.codonTranslate(codon); /* @@@ -541,9 -549,9 +548,9 @@@ { return true; } - if (dnaPos == cdnaSeqChars.length - 3) + if (dnaPos == cdnaSeqChars.length - CODON_LENGTH) { - String codon = String.valueOf(cdnaSeqChars, dnaPos, 3); + String codon = String.valueOf(cdnaSeqChars, dnaPos, CODON_LENGTH); if ("STOP".equals(ResidueProperties.codonTranslate(codon))) { return true; @@@ -894,7 -902,8 +901,8 @@@ } width = Math.max(dnaSeq.getLength(), width); } - int oldwidth, diff; + int oldwidth; + int diff; for (SequenceI dnaSeq : dna.getSequences()) { oldwidth = dnaSeq.getLength(); @@@ -934,9 -943,9 +942,9 @@@ for (AlignedCodonFrame mapping : dnaMappings) { SequenceI peptide = mapping.findAlignedSequence(cdsSeq, protein); - int peptideLength = peptide.getLength(); if (peptide != null) { + int peptideLength = peptide.getLength(); Mapping map = mapping.getMappingBetween(cdsSeq, peptide); if (map != null) { @@@ -950,7 -959,7 +958,7 @@@ .getFromRanges()); int mappedToLength = MappingUtils .getLength(mapList.getToRanges()); - boolean addStopCodon = (cdsLength == mappedFromLength * 3 + 3) + boolean addStopCodon = (cdsLength == mappedFromLength * CODON_LENGTH + CODON_LENGTH) || (peptide.getDatasetSequence().getLength() == mappedFromLength - 1); if (cdsLength != mappedToLength && !addStopCodon) { @@@ -964,8 -973,8 +972,8 @@@ /* * pre-fill the aligned cds sequence with gaps */ - char[] alignedCds = new char[peptideLength * 3 - + (addStopCodon ? 3 : 0)]; + char[] alignedCds = new char[peptideLength * CODON_LENGTH + + (addStopCodon ? CODON_LENGTH : 0)]; Arrays.fill(alignedCds, gapChar); /* @@@ -982,7 -991,7 +990,7 @@@ { if (Comparison.isGap(residue)) { - cdsCol += 3; + cdsCol += CODON_LENGTH; } else { @@@ -991,7 -1000,7 +999,7 @@@ if (codon == null) { // e.g. incomplete start codon, X in peptide - cdsCol += 3; + cdsCol += CODON_LENGTH; } else { @@@ -1009,7 -1018,7 +1017,7 @@@ * append stop codon if not mapped from protein, * closing it up to the end of the mapped sequence */ - if (copiedBases == nucleotides.length - 3) + if (copiedBases == nucleotides.length - CODON_LENGTH) { for (int i = alignedCds.length - 1; i >= 0; i--) { @@@ -1019,7 -1028,7 +1027,7 @@@ break; } } - for (int i = nucleotides.length - 3; i < nucleotides.length; i++) + for (int i = nucleotides.length - CODON_LENGTH; i < nucleotides.length; i++) { alignedCds[cdsCol++] = nucleotides[i]; } @@@ -1680,20 -1689,11 +1688,20 @@@ * didn't find mapped CDS sequence - construct it and add * its dataset sequence to the dataset */ - cdsSeq = makeCdsSequence(dnaSeq.getDatasetSequence(), aMapping); - SequenceI cdsSeqDss = cdsSeq.createDatasetSequence(); + cdsSeq = makeCdsSequence(dnaSeq.getDatasetSequence(), aMapping, + dataset).deriveSequence(); + // cdsSeq has a name constructed as CDS| + // will be either the accession for the coding sequence, + // marked in the /via/ dbref to the protein product accession + // or it will be the original nucleotide accession. + SequenceI cdsSeqDss = cdsSeq.getDatasetSequence(); + cdsSeqs.add(cdsSeq); + if (!dataset.getSequences().contains(cdsSeqDss)) { + // check if this sequence is a newly created one + // so needs adding to the dataset dataset.addSequence(cdsSeqDss); } @@@ -1705,8 -1705,7 +1713,8 @@@ MapList cdsToProteinMap = new MapList(cdsRange, mapList.getToRanges(), mapList.getFromRatio(), mapList.getToRatio()); AlignedCodonFrame cdsToProteinMapping = new AlignedCodonFrame(); - cdsToProteinMapping.addMap(cdsSeq, proteinProduct, cdsToProteinMap); + cdsToProteinMapping.addMap(cdsSeqDss, proteinProduct, + cdsToProteinMap); /* * guard against duplicating the mapping if repeating this action @@@ -1716,8 -1715,23 +1724,8 @@@ mappings.add(cdsToProteinMapping); } - /* - * copy protein's dbrefs to CDS sequence - * this enables Get Cross-References from CDS alignment - */ - DBRefEntry[] proteinRefs = DBRefUtils.selectDbRefs(false, - proteinProduct.getDBRefs()); - if (proteinRefs != null) - { - for (DBRefEntry ref : proteinRefs) - { - DBRefEntry cdsToProteinRef = new DBRefEntry(ref); - cdsToProteinRef.setMap(new Mapping(proteinProduct, - cdsToProteinMap)); - cdsSeqDss.addDBRef(cdsToProteinRef); - } - } - + propagateDBRefsToCDS(cdsSeqDss, dnaSeq.getDatasetSequence(), + proteinProduct, aMapping); /* * add another mapping from original 'from' range to CDS */ @@@ -1725,7 -1739,7 +1733,7 @@@ MapList dnaToCdsMap = new MapList(mapList.getFromRanges(), cdsRange, 1, 1); - dnaToCdsMapping.addMap(dnaSeq.getDatasetSequence(), cdsSeq, + dnaToCdsMapping.addMap(dnaSeq.getDatasetSequence(), cdsSeqDss, dnaToCdsMap); if (!mappings.contains(dnaToCdsMapping)) { @@@ -1739,37 -1753,12 +1747,37 @@@ * same source and accession, so need a different accession for * the CDS from the dna sequence */ - DBRefEntryI dnaRef = dnaDss.getSourceDBRef(); - if (dnaRef != null) + + // specific use case: + // Genomic contig ENSCHR:1, contains coding regions for ENSG01, + // ENSG02, ENSG03, with transcripts and products similarly named. + // cannot add distinct dbrefs mapping location on ENSCHR:1 to ENSG01 + + // JBPNote: ?? can't actually create an example that demonstrates we + // need to + // synthesize an xref. + + for (DBRefEntry primRef : dnaDss.getPrimaryDBRefs()) { + // creates a complementary cross-reference to the source sequence's + // primary reference. + + DBRefEntry cdsCrossRef = new DBRefEntry(primRef.getSource(), + primRef.getSource() + ":" + primRef.getVersion(), + primRef.getAccessionId()); + cdsCrossRef + .setMap(new Mapping(dnaDss, new MapList(dnaToCdsMap))); + cdsSeqDss.addDBRef(cdsCrossRef); + + // problem here is that the cross-reference is synthesized - + // cdsSeq.getName() may be like 'CDS|dnaaccession' or + // 'CDS|emblcdsacc' // assuming cds version same as dna ?!? - DBRefEntry proteinToCdsRef = new DBRefEntry(dnaRef.getSource(), - dnaRef.getVersion(), cdsSeq.getName()); + + DBRefEntry proteinToCdsRef = new DBRefEntry( + primRef.getSource(), primRef.getVersion(), + cdsSeq.getName()); + // proteinToCdsRef.setMap(new Mapping(cdsSeqDss, cdsToProteinMap .getInverse())); proteinProduct.addDBRef(proteinToCdsRef); @@@ -1825,7 -1814,7 +1833,7 @@@ int mappedFromLength = MappingUtils.getLength(aMapping.getMap() .getFromRanges()); int dnaLength = seqDss.getLength(); - if (mappedFromLength == dnaLength || mappedFromLength == dnaLength - 3) + if (mappedFromLength == dnaLength || mappedFromLength == dnaLength - CODON_LENGTH) { return seqDss; } @@@ -1841,7 -1830,7 +1849,7 @@@ for (SequenceToSequenceMapping map : acf.getMappings()) { Mapping mapping = map.getMapping(); - if (mapping != aMapping && mapping.getMap().getFromRatio() == 3 + if (mapping != aMapping && mapping.getMap().getFromRatio() == CODON_LENGTH && proteinProduct == mapping.getTo() && seqDss != map.getFromSeq()) { @@@ -1875,14 -1864,9 +1883,14 @@@ * * @param seq * @param mapping + * @param dataset + * - existing dataset. We check for sequences that look like the CDS + * we are about to construct, if one exists already, then we will + * just return that one. * @return CDS sequence (as a dataset sequence) */ - static SequenceI makeCdsSequence(SequenceI seq, Mapping mapping) + static SequenceI makeCdsSequence(SequenceI seq, Mapping mapping, + AlignmentI dataset) { char[] seqChars = seq.getSequence(); List fromRanges = mapping.getMap().getFromRanges(); @@@ -1909,7 -1893,7 +1917,7 @@@ } } } - + /* * assign 'from id' held in the mapping if set (e.g. EMBL protein_id), * else generate a sequence name @@@ -1917,124 -1901,12 +1925,124 @@@ String mapFromId = mapping.getMappedFromId(); String seqId = "CDS|" + (mapFromId != null ? mapFromId : seq.getName()); SequenceI newSeq = new Sequence(seqId, newSeqChars, 1, newPos); + if (dataset != null) + { + SequenceI[] matches = dataset.findSequenceMatch(newSeq.getName()); + if (matches != null) + { + boolean matched = false; + for (SequenceI mtch : matches) + { + if (mtch.getStart() != newSeq.getStart()) + { + continue; + } + if (mtch.getEnd() != newSeq.getEnd()) + { + continue; + } + if (!Arrays.equals(mtch.getSequence(), newSeq.getSequence())) + { + continue; + } + if (!matched) + { + matched = true; + newSeq = mtch; + } + else + { + System.err + .println("JAL-2154 regression: warning - found (and ignnored a duplicate CDS sequence):" + + mtch.toString()); + } + } + } + } // newSeq.setDescription(mapFromId); return newSeq; } /** + * add any DBRefEntrys to cdsSeq from contig that have a Mapping congruent to + * the given mapping. + * + * @param cdsSeq + * @param contig + * @param mapping + * @return list of DBRefEntrys added. + */ + public static List propagateDBRefsToCDS(SequenceI cdsSeq, + SequenceI contig, SequenceI proteinProduct, Mapping mapping) + { + + // gather direct refs from contig congrent with mapping + List direct = new ArrayList(); + HashSet directSources = new HashSet(); + if (contig.getDBRefs() != null) + { + for (DBRefEntry dbr : contig.getDBRefs()) + { + if (dbr.hasMap() && dbr.getMap().getMap().isTripletMap()) + { + MapList map = dbr.getMap().getMap(); + // check if map is the CDS mapping + if (mapping.getMap().equals(map)) + { + direct.add(dbr); + directSources.add(dbr.getSource()); + } + } + } + } + DBRefEntry[] onSource = DBRefUtils.selectRefs( + proteinProduct.getDBRefs(), + directSources.toArray(new String[0])); + List propagated = new ArrayList(); + + // and generate appropriate mappings + for (DBRefEntry cdsref : direct) + { + // clone maplist and mapping + MapList cdsposmap = new MapList(Arrays.asList(new int[][] { new int[] + { cdsSeq.getStart(), cdsSeq.getEnd() } }), cdsref.getMap().getMap() + .getToRanges(), 3, 1); + Mapping cdsmap = new Mapping(cdsref.getMap().getTo(), cdsref.getMap() + .getMap()); + + // create dbref + DBRefEntry newref = new DBRefEntry(cdsref.getSource(), + cdsref.getVersion(), cdsref.getAccessionId(), new Mapping( + cdsmap.getTo(), cdsposmap)); + + // and see if we can map to the protein product for this mapping. + // onSource is the filtered set of accessions on protein that we are + // tranferring, so we assume accession is the same. + if (cdsmap.getTo() == null && onSource != null) + { + List sourceRefs = DBRefUtils.searchRefs(onSource, + cdsref.getAccessionId()); + if (sourceRefs != null) + { + for (DBRefEntry srcref : sourceRefs) + { + if (srcref.getSource().equalsIgnoreCase(cdsref.getSource())) + { + // we have found a complementary dbref on the protein product, so + // update mapping's getTo + newref.getMap().setTo(proteinProduct); + } + } + } + } + cdsSeq.addDBRef(newref); + propagated.add(newref); + } + return propagated; + } + + /** * Transfers co-located features on 'fromSeq' to 'toSeq', adjusting the * feature start/end ranges, optionally omitting specified feature types. * Returns the number of features copied. @@@ -2163,7 -2035,7 +2171,7 @@@ /* * dna length should map to protein (or protein plus stop codon) */ - int codesForResidues = mappedDnaLength / 3; + int codesForResidues = mappedDnaLength / CODON_LENGTH; if (codesForResidues == (proteinLength + 1)) { // assuming extra codon is for STOP and not in peptide @@@ -2172,7 -2044,7 +2180,7 @@@ if (codesForResidues == proteinLength) { proteinRange.add(new int[] { proteinStart, proteinEnd }); - return new MapList(ranges, proteinRange, 3, 1); + return new MapList(ranges, proteinRange, CODON_LENGTH, 1); } return null; } @@@ -2448,7 -2320,7 +2456,7 @@@ * are currently ignored here */ String trans = codon.contains("-") ? "-" - : (codon.length() > 3 ? null : ResidueProperties + : (codon.length() > CODON_LENGTH ? null : ResidueProperties .codonTranslate(codon)); if (trans != null && !trans.equals(residue)) { @@@ -2460,7 -2332,7 +2468,7 @@@ // set score to 0f so 'graduated colour' option is offered! JAL-2060 SequenceFeature sf = new SequenceFeature( SequenceOntologyI.SEQUENCE_VARIANT, desc, peptidePos, - peptidePos, 0f, "Jalview"); + peptidePos, 0f, var.getSource()); StringBuilder attributes = new StringBuilder(32); String id = (String) var.variant.getValue(ID); if (id != null) @@@ -2471,7 -2343,7 +2479,7 @@@ } sf.setValue(ID, id); attributes.append(ID).append("=").append(id); - // TODO handle other species variants + // TODO handle other species variants JAL-2064 StringBuilder link = new StringBuilder(32); try { @@@ -2510,6 -2382,7 +2518,7 @@@ * @param dnaToProtein * @return */ + @SuppressWarnings("unchecked") static LinkedHashMap[]> buildDnaVariantsMap( SequenceI dnaSeq, MapList dnaToProtein) { @@@ -2553,7 -2426,7 +2562,7 @@@ List[] codonVariants = variants.get(peptidePosition); if (codonVariants == null) { - codonVariants = new ArrayList[3]; + codonVariants = new ArrayList[CODON_LENGTH]; codonVariants[0] = new ArrayList(); codonVariants[1] = new ArrayList(); codonVariants[2] = new ArrayList(); @@@ -2587,7 -2460,7 +2596,7 @@@ /* * save nucleotide (and any variant) for each codon position */ - for (int codonPos = 0; codonPos < 3; codonPos++) + for (int codonPos = 0; codonPos < CODON_LENGTH; codonPos++) { String nucleotide = String.valueOf( dnaSeq.getCharAt(codon[codonPos] - dnaStart)) @@@ -2640,7 -2513,7 +2649,7 @@@ { AlignmentI copy = new Alignment(new Alignment(seqs)); copy.setDataset(dataset); - + boolean isProtein = !copy.isNucleotide(); SequenceIdMatcher matcher = new SequenceIdMatcher(seqs); if (xrefs != null) { @@@ -2651,8 -2524,7 +2660,8 @@@ { for (DBRefEntry dbref : dbrefs) { - if (dbref.getMap() == null || dbref.getMap().getTo() == null) + if (dbref.getMap() == null || dbref.getMap().getTo() == null + || dbref.getMap().getTo().isProtein() != isProtein) { continue; } diff --combined src/jalview/ext/ensembl/EnsemblSeqProxy.java index 5a32736,cc002e1..5fccedd --- a/src/jalview/ext/ensembl/EnsemblSeqProxy.java +++ b/src/jalview/ext/ensembl/EnsemblSeqProxy.java @@@ -276,7 -276,8 +276,7 @@@ public abstract class EnsemblSeqProxy e { // clunky: ensure Uniprot xref if we have one is on mapped sequence SequenceI ds = proteinSeq.getDatasetSequence(); - ds.setSourceDBRef(proteinSeq.getSourceDBRef()); - + // TODO: Verify ensp primary ref is on proteinSeq.getDatasetSequence() Mapping map = new Mapping(ds, mapList); DBRefEntry dbr = new DBRefEntry(getDbSource(), getEnsemblDataVersion(), proteinSeq.getName(), map); @@@ -308,8 -309,7 +308,8 @@@ seq = seq.getDatasetSequence(); } - EnsemblXref xrefFetcher = new EnsemblXref(getDomain()); + EnsemblXref xrefFetcher = new EnsemblXref(getDomain(), getDbSource(), + getEnsemblDataVersion()); List xrefs = xrefFetcher.getCrossReferences(seq.getName()); for (DBRefEntry xref : xrefs) { @@@ -322,6 -322,7 +322,6 @@@ DBRefEntry self = new DBRefEntry(getDbSource(), getEnsemblDataVersion(), seq.getName()); seq.addDBRef(self); - seq.setSourceDBRef(self); } /** @@@ -381,7 -382,7 +381,7 @@@ { DBRefEntry dbref = DBRefUtils.parseToDbRef(sq, getDbSource(), getEnsemblDataVersion(), name); - sq.setSourceDBRef(dbref); + sq.addDBRef(dbref); } } if (alignment == null) @@@ -612,6 -613,10 +612,10 @@@ SequenceFeature copy = new SequenceFeature(sf); copy.setBegin(Math.min(mappedRange[0], mappedRange[1])); copy.setEnd(Math.max(mappedRange[0], mappedRange[1])); + if (".".equals(copy.getFeatureGroup())) + { + copy.setFeatureGroup(getDbSource()); + } targetSequence.addSequenceFeature(copy); /* diff --combined test/jalview/analysis/AlignmentUtilsTests.java index 7e8442d,a856231..ddd38e7 --- a/test/jalview/analysis/AlignmentUtilsTests.java +++ b/test/jalview/analysis/AlignmentUtilsTests.java @@@ -994,44 -994,29 +994,44 @@@ public class AlignmentUtilsTest /* * need a sourceDbRef if we are to construct dbrefs to the CDS - * sequence + * sequence from the dna contig sequences */ DBRefEntry dbref = new DBRefEntry("ENSEMBL", "0", "dna1"); - dna1.getDatasetSequence().setSourceDBRef(dbref); + dna1.getDatasetSequence().addDBRef(dbref); + org.testng.Assert.assertEquals(dbref, dna1.getPrimaryDBRefs().get(0)); dbref = new DBRefEntry("ENSEMBL", "0", "dna2"); - dna2.getDatasetSequence().setSourceDBRef(dbref); + dna2.getDatasetSequence().addDBRef(dbref); + org.testng.Assert.assertEquals(dbref, dna2.getPrimaryDBRefs().get(0)); /* * CDS sequences are 'discovered' from dna-to-protein mappings on the alignment * dataset (e.g. added from dbrefs by CrossRef.findXrefSequences) */ - MapList map = new MapList(new int[] { 4, 6, 10, 12 }, + MapList mapfordna1 = new MapList(new int[] { 4, 6, 10, 12 }, new int[] { 1, 2 }, 3, 1); AlignedCodonFrame acf = new AlignedCodonFrame(); - acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map); + acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), + mapfordna1); dna.addCodonFrame(acf); - map = new MapList(new int[] { 1, 3, 7, 9, 13, 15 }, new int[] { 1, 3 }, + MapList mapfordna2 = new MapList(new int[] { 1, 3, 7, 9, 13, 15 }, + new int[] { 1, 3 }, 3, 1); acf = new AlignedCodonFrame(); - acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(), map); + acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(), + mapfordna2); dna.addCodonFrame(acf); /* + * In this case, mappings originally came from matching Uniprot accessions - so need an xref on dna involving those regions. These are normally constructed from CDS annotation + */ + DBRefEntry dna1xref = new DBRefEntry("UNIPROT", "ENSEMBL", "pep1", + new Mapping(mapfordna1)); + dna1.getDatasetSequence().addDBRef(dna1xref); + DBRefEntry dna2xref = new DBRefEntry("UNIPROT", "ENSEMBL", "pep2", + new Mapping(mapfordna2)); + dna2.getDatasetSequence().addDBRef(dna2xref); + + /* * execute method under test: */ AlignmentI cds = AlignmentUtils.makeCdsAlignment(new SequenceI[] { @@@ -1057,12 -1042,11 +1057,12 @@@ * verify CDS has a dbref with mapping to peptide */ assertNotNull(cds1Dss.getDBRefs()); - assertEquals(1, cds1Dss.getDBRefs().length); + assertEquals(2, cds1Dss.getDBRefs().length); dbref = cds1Dss.getDBRefs()[0]; - assertEquals("UNIPROT", dbref.getSource()); - assertEquals("0", dbref.getVersion()); - assertEquals("pep1", dbref.getAccessionId()); + assertEquals(dna1xref.getSource(), dbref.getSource()); + // version is via ensembl's primary ref + assertEquals(dna1xref.getVersion(), dbref.getVersion()); + assertEquals(dna1xref.getAccessionId(), dbref.getAccessionId()); assertNotNull(dbref.getMap()); assertSame(pep1.getDatasetSequence(), dbref.getMap().getTo()); MapList cdsMapping = new MapList(new int[] { 1, 6 }, @@@ -1073,7 -1057,6 +1073,7 @@@ * verify peptide has added a dbref with reverse mapping to CDS */ assertNotNull(pep1.getDBRefs()); + // FIXME pep1.getDBRefs() is 1 - is that the correct behaviour ? assertEquals(2, pep1.getDBRefs().length); dbref = pep1.getDBRefs()[1]; assertEquals("ENSEMBL", dbref.getSource()); @@@ -1954,13 -1937,15 +1954,15 @@@ public void testComputePeptideVariants() { /* - * scenario: AAATTTCCC codes for KFP, with variants - * GAA -> E - * CAA -> Q - * AAG synonymous - * AAT -> N - * TTC synonymous - * CAC,CGC -> H,R (as one variant) + * scenario: AAATTTCCC codes for KFP + * variants: + * GAA -> E source: Ensembl + * CAA -> Q source: dbSNP + * AAG synonymous source: COSMIC + * AAT -> N source: Ensembl + * ...TTC synonymous source: dbSNP + * ......CAC,CGC -> H,R source: COSMIC + * (one variant with two alleles) */ SequenceI peptide = new Sequence("pep/10-12", "KFP"); @@@ -1968,32 -1953,35 +1970,35 @@@ * two distinct variants for codon 1 position 1 * second one has clinical significance */ + String ensembl = "Ensembl"; + String dbSnp = "dbSNP"; + String cosmic = "COSMIC"; SequenceFeature sf1 = new SequenceFeature("sequence_variant", "", 1, 1, - 0f, null); + 0f, ensembl); sf1.setValue("alleles", "A,G"); // GAA -> E sf1.setValue("ID", "var1.125A>G"); SequenceFeature sf2 = new SequenceFeature("sequence_variant", "", 1, 1, - 0f, null); + 0f, dbSnp); sf2.setValue("alleles", "A,C"); // CAA -> Q sf2.setValue("ID", "var2"); sf2.setValue("clinical_significance", "Dodgy"); SequenceFeature sf3 = new SequenceFeature("sequence_variant", "", 3, 3, - 0f, null); + 0f, cosmic); sf3.setValue("alleles", "A,G"); // synonymous sf3.setValue("ID", "var3"); sf3.setValue("clinical_significance", "None"); SequenceFeature sf4 = new SequenceFeature("sequence_variant", "", 3, 3, - 0f, null); + 0f, ensembl); sf4.setValue("alleles", "A,T"); // AAT -> N sf4.setValue("ID", "sequence_variant:var4"); // prefix gets stripped off sf4.setValue("clinical_significance", "Benign"); SequenceFeature sf5 = new SequenceFeature("sequence_variant", "", 6, 6, - 0f, null); + 0f, dbSnp); sf5.setValue("alleles", "T,C"); // synonymous sf5.setValue("ID", "var5"); sf5.setValue("clinical_significance", "Bad"); SequenceFeature sf6 = new SequenceFeature("sequence_variant", "", 8, 8, - 0f, null); + 0f, cosmic); sf6.setValue("alleles", "C,A,G"); // CAC,CGC -> H,R sf6.setValue("ID", "var6"); sf6.setValue("clinical_significance", "Good"); @@@ -2041,14 -2029,15 +2046,15 @@@ /* * verify added sequence features for - * var1 K -> E - * var2 K -> Q - * var4 K -> N - * var6 P -> H - * var6 P -> R + * var1 K -> E Ensembl + * var2 K -> Q dbSNP + * var4 K -> N Ensembl + * var6 P -> H COSMIC + * var6 P -> R COSMIC */ SequenceFeature[] sfs = peptide.getSequenceFeatures(); assertEquals(5, sfs.length); + SequenceFeature sf = sfs[0]; assertEquals(1, sf.getBegin()); assertEquals(1, sf.getEnd()); @@@ -2061,7 -2050,8 +2067,8 @@@ assertEquals( "p.Lys1Glu var1.125A>G|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var1.125A%3EG", sf.links.get(0)); - assertEquals("Jalview", sf.getFeatureGroup()); + assertEquals(ensembl, sf.getFeatureGroup()); + sf = sfs[1]; assertEquals(1, sf.getBegin()); assertEquals(1, sf.getEnd()); @@@ -2073,7 -2063,8 +2080,8 @@@ assertEquals( "p.Lys1Gln var2|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var2", sf.links.get(0)); - assertEquals("Jalview", sf.getFeatureGroup()); + assertEquals(dbSnp, sf.getFeatureGroup()); + sf = sfs[2]; assertEquals(1, sf.getBegin()); assertEquals(1, sf.getEnd()); @@@ -2085,7 -2076,9 +2093,9 @@@ assertEquals( "p.Lys1Asn var4|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var4", sf.links.get(0)); - assertEquals("Jalview", sf.getFeatureGroup()); + assertEquals(ensembl, sf.getFeatureGroup()); + + // var5 generates two distinct protein variant features sf = sfs[3]; assertEquals(3, sf.getBegin()); assertEquals(3, sf.getEnd()); @@@ -2097,8 -2090,8 +2107,8 @@@ assertEquals( "p.Pro3His var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6", sf.links.get(0)); - // var5 generates two distinct protein variant features - assertEquals("Jalview", sf.getFeatureGroup()); + assertEquals(cosmic, sf.getFeatureGroup()); + sf = sfs[4]; assertEquals(3, sf.getBegin()); assertEquals(3, sf.getEnd()); @@@ -2110,7 -2103,7 +2120,7 @@@ assertEquals( "p.Pro3Arg var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6", sf.links.get(0)); - assertEquals("Jalview", sf.getFeatureGroup()); + assertEquals(cosmic, sf.getFeatureGroup()); } /**