X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblGene.java;h=edeeeddb08d5ac7ebc5d6708a30f60df29e94de1;hb=3d0101179759ef157b088ea135423cd909512d9f;hp=df4e45a7e07fdb9f0d11a836755e10964c11ace8;hpb=c406d789d51e6ac1ff45e3568d37e9ed53025f03;p=jalview.git diff --git a/src/jalview/ext/ensembl/EnsemblGene.java b/src/jalview/ext/ensembl/EnsemblGene.java index df4e45a..edeeedd 100644 --- a/src/jalview/ext/ensembl/EnsemblGene.java +++ b/src/jalview/ext/ensembl/EnsemblGene.java @@ -1,16 +1,40 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.ext.ensembl; -import jalview.api.FeatureSettingsI; +import jalview.api.FeatureColourI; +import jalview.api.FeatureSettingsModelI; import jalview.datamodel.AlignmentI; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import jalview.io.gff.SequenceOntologyFactory; import jalview.io.gff.SequenceOntologyI; -import jalview.schemes.FeatureColourScheme; +import jalview.schemes.FeatureColour; +import jalview.schemes.FeatureSettingsAdapter; import jalview.util.MapList; -import jalview.util.StringUtils; +import java.awt.Color; +import java.io.UnsupportedEncodingException; +import java.net.URLDecoder; import java.util.ArrayList; import java.util.Arrays; import java.util.List; @@ -37,10 +61,28 @@ public class EnsemblGene extends EnsemblSeqProxy EnsemblFeatureType.exon, EnsemblFeatureType.cds, EnsemblFeatureType.variation }; + /** + * Default constructor (to use rest.ensembl.org) + */ + public EnsemblGene() + { + super(); + } + + /** + * Constructor given the target domain to fetch data from + * + * @param d + */ + public EnsemblGene(String d) + { + super(d); + } + @Override public String getDbName() { - return "ENSEMBL (GENE)"; + return "ENSEMBL"; } @Override @@ -67,7 +109,8 @@ public class EnsemblGene extends EnsemblSeqProxy *
  • resolves an external identifier by looking up xref-ed gene ids
    • *
  • fetches the gene sequence
    • *
  • fetches features on the sequence
    • - *
  • identifies "transcript" features whose Parent is the requested gene
    • + *
  • identifies "transcript" features whose Parent is the requested + * gene
    • *
  • fetches the transcript sequence for each transcript
    • *
  • makes a mapping from the gene to each transcript
    • *
  • copies features from gene to transcript sequences
    • @@ -78,56 +121,110 @@ public class EnsemblGene extends EnsemblSeqProxy * * * @param query - * one or more identifiers separated by a space - * @return an alignment containing one or more genes, and possibly - * transcripts, or null + * a single gene or transcript identifier or gene name + * @return an alignment containing a gene, and possibly transcripts, or null */ @Override public AlignmentI getSequenceRecords(String query) throws Exception { - // todo: tidy up handling of one or multiple accession ids - String[] queries = query.split(getAccessionSeparator()); - /* - * if given a transcript id, look up its gene parent + * convert to a non-duplicated list of gene identifiers */ - if (isTranscriptIdentifier(query)) + List geneIds = getGeneIds(query); + + AlignmentI al = null; + for (String geneId : geneIds) { - // we are assuming all transcripts have the same gene parent here - query = new EnsemblLookup().getParent(queries[0]); - if (query == null) + /* + * fetch the gene sequence(s) with features and xrefs + */ + AlignmentI geneAlignment = super.getSequenceRecords(geneId); + if (geneAlignment == null) { - return null; + continue; + } + if (geneAlignment.getHeight() == 1) + { + getTranscripts(geneAlignment, geneId); + } + if (al == null) + { + al = geneAlignment; + } + else + { + al.append(geneAlignment); } } + return al; + } - /* - * if given a gene or other external name, lookup and fetch - * the corresponding gene for all model organisms - */ - if (!isGeneIdentifier(query)) + /** + * Converts a query, which may contain one or more gene or transcript + * identifiers, into a non-redundant list of gene identifiers. + * + * @param accessions + * @return + */ + List getGeneIds(String accessions) + { + List geneIds = new ArrayList(); + + for (String acc : accessions.split(getAccessionSeparator())) { - List geneIds = new EnsemblSymbol().getIds(query); - if (geneIds.isEmpty()) + if (isGeneIdentifier(acc)) { - return null; + if (!geneIds.contains(acc)) + { + geneIds.add(acc); + } } - String theIds = StringUtils.listToDelimitedString(geneIds, - getAccessionSeparator()); - return getSequenceRecords(theIds); - } - AlignmentI al = super.getSequenceRecords(query); + /* + * if given a transcript id, look up its gene parent + */ + else if (isTranscriptIdentifier(acc)) + { + String geneId = new EnsemblLookup(getDomain()).getParent(acc); + if (geneId != null && !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 we retrieved a single gene, get its transcripts as well - */ - if (al.getHeight() == 1) - { - getTranscripts(al, query); + 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 + { + List ids = new EnsemblSymbol(getDomain(), getDbSource(), + getDbVersion()).getIds(acc); + for (String geneId : ids) + { + if (!geneIds.contains(geneId)) + { + geneIds.add(geneId); + } + } + } } - - return al; + return geneIds; } /** @@ -139,7 +236,8 @@ public class EnsemblGene extends EnsemblSeqProxy */ protected String getGeneIdentifiersForName(String query) { - List ids = new EnsemblSymbol().getIds(query); + List ids = new EnsemblSymbol(getDomain(), getDbSource(), + getDbVersion()).getIds(query); if (ids != null) { for (String id : ids) @@ -173,6 +271,35 @@ public class EnsemblGene extends EnsemblSeqProxy { makeTranscript(transcriptFeature, al, gene); } + + clearGeneFeatures(gene); + } + + /** + * Remove unwanted features (transcript, exon, CDS) from the gene sequence + * after we have used them to derive transcripts and transfer features + * + * @param gene + */ + protected void clearGeneFeatures(SequenceI gene) + { + SequenceFeature[] sfs = gene.getSequenceFeatures(); + if (sfs != null) + { + SequenceOntologyI so = SequenceOntologyFactory.getInstance(); + List filtered = new ArrayList(); + for (SequenceFeature sf : sfs) + { + String type = sf.getType(); + if (!isTranscript(type) && !so.isA(type, SequenceOntologyI.EXON) + && !so.isA(type, SequenceOntologyI.CDS)) + { + filtered.add(sf); + } + } + gene.setSequenceFeatures( + filtered.toArray(new SequenceFeature[filtered.size()])); + } } /** @@ -188,8 +315,8 @@ public class EnsemblGene extends EnsemblSeqProxy * the parent gene sequence, with features * @return */ - SequenceI makeTranscript(SequenceFeature transcriptFeature, - AlignmentI al, SequenceI gene) + SequenceI makeTranscript(SequenceFeature transcriptFeature, AlignmentI al, + SequenceI gene) { String accId = getTranscriptId(transcriptFeature); if (accId == null) @@ -237,11 +364,27 @@ public class EnsemblGene extends EnsemblSeqProxy mappedFrom.add(new int[] { sf.getBegin(), sf.getEnd() }); } - Sequence transcript = new Sequence(accId, seqChars, 1, transcriptLength); - String geneName = (String) transcriptFeature.getValue(NAME); - if (geneName != null) + Sequence transcript = new Sequence(accId, seqChars, 1, + transcriptLength); + + /* + * Ensembl has gene name as transcript Name + * EnsemblGenomes doesn't, but has a url-encoded description field + */ + String description = (String) transcriptFeature.getValue(NAME); + if (description == null) + { + description = (String) transcriptFeature.getValue(DESCRIPTION); + } + if (description != null) { - transcript.setDescription(geneName); + try + { + transcript.setDescription(URLDecoder.decode(description, "UTF-8")); + } catch (UnsupportedEncodingException e) + { + e.printStackTrace(); // as if + } } transcript.createDatasetSequence(); @@ -254,18 +397,19 @@ public class EnsemblGene extends EnsemblSeqProxy List mapTo = new ArrayList(); mapTo.add(new int[] { 1, transcriptLength }); MapList mapping = new MapList(mappedFrom, mapTo, 1, 1); - new EnsemblCdna().transferFeatures(gene.getSequenceFeatures(), + EnsemblCdna cdna = new EnsemblCdna(getDomain()); + cdna.transferFeatures(gene.getSequenceFeatures(), transcript.getDatasetSequence(), mapping, parentId); /* * fetch and save cross-references */ - super.getCrossReferences(transcript); + cdna.getCrossReferences(transcript); /* * and finally fetch the protein product and save as a cross-reference */ - new EnsemblCdna().addProteinProduct(transcript); + cdna.addProteinProduct(transcript); return transcript; } @@ -362,13 +506,13 @@ public class EnsemblGene extends EnsemblSeqProxy @Override protected boolean retainFeature(SequenceFeature sf, String accessionId) { - if (SequenceOntologyFactory.getInstance().isA(sf.getType(), - SequenceOntologyI.GENE)) + SequenceOntologyI so = SequenceOntologyFactory.getInstance(); + String type = sf.getType(); + if (so.isA(type, SequenceOntologyI.GENE)) { return false; } - - if (isTranscript(sf.getType())) + if (isTranscript(type)) { String parent = (String) sf.getValue(PARENT); if (!(GENE_PREFIX + accessionId).equals(parent)) @@ -390,15 +534,6 @@ public class EnsemblGene extends EnsemblSeqProxy return false; } - @Override - protected List getCrossReferenceDatabases() - { - // found these for ENSG00000157764 on 30/01/2016: - // return new String[] {"Vega_gene", "OTTG", "ENS_LRG_gene", "ArrayExpress", - // "EntrezGene", "HGNC", "MIM_GENE", "MIM_MORBID", "WikiGene"}; - return super.getCrossReferenceDatabases(); - } - /** * Override to do nothing as Ensembl doesn't return a protein sequence for a * gene identifier @@ -414,10 +549,84 @@ public class EnsemblGene extends EnsemblSeqProxy return ACCESSION_REGEX; } + /** + * Returns a descriptor for suitable feature display settings with + *
      + *
    • only exon or sequence_variant features (or their subtypes in the + * Sequence Ontology) visible
      • + *
    • variant features coloured red
      • + *
    • exon features coloured by label (exon name)
      • + *
    • variants displayed above (on top of) exons
      • + *
    + */ @Override - public FeatureSettingsI getFeatureColourScheme() + public FeatureSettingsModelI getFeatureColourScheme() { - return FeatureColourScheme.EnsemblVariants; + return new FeatureSettingsAdapter() + { + SequenceOntologyI so = SequenceOntologyFactory.getInstance(); + + @Override + public boolean isFeatureDisplayed(String type) + { + return (so.isA(type, SequenceOntologyI.EXON) + || so.isA(type, SequenceOntologyI.SEQUENCE_VARIANT)); + } + + @Override + public FeatureColourI getFeatureColour(String type) + { + if (so.isA(type, SequenceOntologyI.EXON)) + { + return new FeatureColour() + { + @Override + public boolean isColourByLabel() + { + return true; + } + }; + } + if (so.isA(type, SequenceOntologyI.SEQUENCE_VARIANT)) + { + return new FeatureColour() + { + + @Override + public Color getColour() + { + return Color.RED; + } + }; + } + return null; + } + + /** + * order to render sequence_variant after exon after the rest + */ + @Override + public int compare(String feature1, String feature2) + { + if (so.isA(feature1, SequenceOntologyI.SEQUENCE_VARIANT)) + { + return +1; + } + if (so.isA(feature2, SequenceOntologyI.SEQUENCE_VARIANT)) + { + return -1; + } + if (so.isA(feature1, SequenceOntologyI.EXON)) + { + return +1; + } + if (so.isA(feature2, SequenceOntologyI.EXON)) + { + return -1; + } + return 0; + } + }; } }