X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblGene.java;h=afff4c2630609be55291630e560b3c23e0bdbf05;hb=a57976ba40e1abe6d7c1940386e1a25419ef9c9d;hp=f975ac8b7b214460c54a8db7fa08c41a14d9c93b;hpb=a774a016b6c07368e9e99d4568199f768a77d42f;p=jalview.git diff --git a/src/jalview/ext/ensembl/EnsemblGene.java b/src/jalview/ext/ensembl/EnsemblGene.java index f975ac8..afff4c2 100644 --- a/src/jalview/ext/ensembl/EnsemblGene.java +++ b/src/jalview/ext/ensembl/EnsemblGene.java @@ -23,7 +23,8 @@ package jalview.ext.ensembl; import jalview.api.FeatureColourI; import jalview.api.FeatureSettingsModelI; import jalview.datamodel.AlignmentI; -import jalview.datamodel.GeneLoci; +import jalview.datamodel.DBRefEntry; +import jalview.datamodel.GeneLociI; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; @@ -145,6 +146,9 @@ public class EnsemblGene extends EnsemblSeqProxy { continue; } + + parseChromosomeLocations(geneAlignment); + if (geneAlignment.getHeight() == 1) { getTranscripts(geneAlignment, geneId); @@ -162,8 +166,48 @@ public class EnsemblGene extends EnsemblSeqProxy } /** - * Converts a query, which may contain one or more gene or transcript - * identifiers, into a non-redundant list of gene identifiers. + * Parses and saves fields of an Ensembl-style description e.g. + * chromosome:GRCh38:17:45051610:45109016:1 + * + * @param alignment + */ + private void parseChromosomeLocations(AlignmentI alignment) + { + for (SequenceI seq : alignment.getSequences()) + { + String description = seq.getDescription(); + if (description == null) + { + continue; + } + String[] tokens = description.split(":"); + if (tokens.length == 6 && tokens[0].startsWith(DBRefEntry.CHROMOSOME)) + { + String ref = tokens[1]; + String chrom = tokens[2]; + try + { + int chStart = Integer.parseInt(tokens[3]); + int chEnd = Integer.parseInt(tokens[4]); + boolean forwardStrand = "1".equals(tokens[5]); + String species = ""; // dunno yet! + int[] from = new int[] { seq.getStart(), seq.getEnd() }; + int[] to = new int[] { forwardStrand ? chStart : chEnd, + forwardStrand ? chEnd : chStart }; + MapList map = new MapList(from, to, 1, 1); + seq.setGeneLoci(species, ref, chrom, map); + } catch (NumberFormatException e) + { + System.err.println("Bad integers in description " + description); + } + } + } + } + + /** + * Converts a query, which may contain one or more gene, transcript, or + * external (to Ensembl) identifiers, into a non-redundant list of gene + * identifiers. * * @param accessions * @return @@ -174,54 +218,30 @@ public class EnsemblGene extends EnsemblSeqProxy for (String acc : accessions.split(getAccessionSeparator())) { - if (isGeneIdentifier(acc)) - { - if (!geneIds.contains(acc)) - { - geneIds.add(acc); - } - } - /* - * if given a transcript id, look up its gene parent + * First try lookup as an Ensembl (gene or transcript) identifier */ - else if (isTranscriptIdentifier(acc)) + String geneId = new EnsemblLookup(getDomain()).getGeneId(acc); + if (geneId != null) { - String geneId = new EnsemblLookup(getDomain()).getParent(acc); - if (geneId != null && !geneIds.contains(geneId)) + if (!geneIds.contains(geneId)) { geneIds.add(geneId); } } - else if (isProteinIdentifier(acc)) - { - String tscriptId = new EnsemblLookup(getDomain()).getParent(acc); - if (tscriptId != null) - { - String geneId = new EnsemblLookup(getDomain()) - .getParent(tscriptId); - - if (geneId != null && !geneIds.contains(geneId)) - { - geneIds.add(geneId); - } - } - // NOTE - acc is lost if it resembles an ENS.+ ID but isn't actually - // resolving to one... e.g. ENSMICP00000009241 - } - /* - * if given a gene or other external name, lookup and fetch - * the corresponding gene for all model organisms - */ else { + /* + * if given a gene or other external name, lookup and fetch + * the corresponding gene for all model organisms + */ List ids = new EnsemblSymbol(getDomain(), getDbSource(), - getDbVersion()).getIds(acc); - for (String geneId : ids) + getDbVersion()).getGeneIds(acc); + for (String id : ids) { - if (!geneIds.contains(geneId)) + if (!geneIds.contains(id)) { - geneIds.add(geneId); + geneIds.add(id); } } } @@ -230,30 +250,6 @@ public class EnsemblGene extends EnsemblSeqProxy } /** - * Attempts to get Ensembl stable identifiers for model organisms for a gene - * name by calling the xrefs symbol REST service to resolve the gene name. - * - * @param query - * @return - */ - protected String getGeneIdentifiersForName(String query) - { - List ids = new EnsemblSymbol(getDomain(), getDbSource(), - getDbVersion()).getIds(query); - if (ids != null) - { - for (String id : ids) - { - if (isGeneIdentifier(id)) - { - return id; - } - } - } - return null; - } - - /** * Constructs all transcripts for the gene, as identified by "transcript" * features whose Parent is the requested gene. The coding transcript * sequences (i.e. with introns omitted) are added to the alignment. @@ -426,40 +422,31 @@ public class EnsemblGene extends EnsemblSeqProxy * @param mapping * the mapping from gene to transcript positions */ - protected void mapTranscriptToChromosome(Sequence transcript, + protected void mapTranscriptToChromosome(SequenceI transcript, SequenceI gene, MapList mapping) { - GeneLoci loci = ((Sequence) gene).getGeneLoci(); + GeneLociI loci = gene.getGeneLoci(); if (loci == null) { return; } - /* - * patch to ensure gene to chromosome mapping is complete - * (in case created before gene length was known) - */ - MapList geneMapping = loci.mapping; - if (geneMapping.getFromRanges().get(0)[1] == 0) - { - geneMapping.getFromRanges().get(0)[0] = gene.getStart(); - geneMapping.getFromRanges().get(0)[1] = gene.getEnd(); - } + MapList geneMapping = loci.getMap(); List exons = mapping.getFromRanges(); List transcriptLoci = new ArrayList<>(); - - for (int[] exon : exons) { + + for (int[] exon : exons) + { transcriptLoci.add(geneMapping.locateInTo(exon[0], exon[1])); } List transcriptRange = Arrays.asList(new int[] { transcript.getStart(), transcript.getEnd() }); MapList mapList = new MapList(transcriptRange, transcriptLoci, 1, 1); - GeneLoci gl = new GeneLoci(loci.species, loci.assembly, - loci.chromosome, mapList); - transcript.setGeneLoci(gl); + transcript.setGeneLoci(loci.getSpeciesId(), loci.getAssemblyId(), + loci.getChromosomeId(), mapList); } /** @@ -476,6 +463,12 @@ public class EnsemblGene extends EnsemblSeqProxy /** * Returns a list of the transcript features on the sequence whose Parent is * the gene for the accession id. + *

+ * Transcript features are those of type "transcript", or any of its sub-types + * in the Sequence Ontology e.g. "mRNA", "processed_transcript". We also + * include "NMD_transcript_variant", because this type behaves like a + * transcript identifier in Ensembl, although strictly speaking it is not in + * the SO. * * @param accId * @param geneSequence @@ -487,19 +480,18 @@ public class EnsemblGene extends EnsemblSeqProxy List transcriptFeatures = new ArrayList(); String parentIdentifier = GENE_PREFIX + accId; - // todo optimise here by transcript type! + List sfs = geneSequence.getFeatures() - .getPositionalFeatures(); + .getFeaturesByOntology(SequenceOntologyI.TRANSCRIPT); + sfs.addAll(geneSequence.getFeatures().getPositionalFeatures( + SequenceOntologyI.NMD_TRANSCRIPT_VARIANT)); for (SequenceFeature sf : sfs) { - if (isTranscript(sf.getType())) + String parent = (String) sf.getValue(PARENT); + if (parentIdentifier.equals(parent)) { - String parent = (String) sf.getValue(PARENT); - if (parentIdentifier.equals(parent)) - { - transcriptFeatures.add(sf); - } + transcriptFeatures.add(sf); } }