X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblSeqProxy.java;h=f96f1d5a4f36ad9c42349782b9031477365678c6;hb=f59dd9efbb3dfc313ab0b0507832e21cd0076fe1;hp=2d0e3fe93034eecfc9a7c976d189a0fcc83573e0;hpb=4816a1eeeec4c5b9ff845a711b2e10d621aed6e8;p=jalview.git diff --git a/src/jalview/ext/ensembl/EnsemblSeqProxy.java b/src/jalview/ext/ensembl/EnsemblSeqProxy.java index 2d0e3fe..f96f1d5 100644 --- a/src/jalview/ext/ensembl/EnsemblSeqProxy.java +++ b/src/jalview/ext/ensembl/EnsemblSeqProxy.java @@ -28,27 +28,32 @@ import jalview.datamodel.AlignmentI; import jalview.datamodel.DBRefEntry; import jalview.datamodel.DBRefSource; import jalview.datamodel.Mapping; +import jalview.datamodel.Sequence; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; +import jalview.datamodel.features.SequenceFeatures; import jalview.exceptions.JalviewException; -import jalview.io.FastaFile; -import jalview.io.FileParse; +import jalview.io.gff.Gff3Helper; import jalview.io.gff.SequenceOntologyFactory; import jalview.io.gff.SequenceOntologyI; import jalview.util.Comparison; import jalview.util.DBRefUtils; +import jalview.util.IntRangeComparator; import jalview.util.MapList; -import jalview.util.RangeComparator; +import java.io.BufferedReader; import java.io.IOException; import java.net.MalformedURLException; import java.net.URL; import java.util.ArrayList; import java.util.Arrays; import java.util.Collections; -import java.util.Comparator; import java.util.List; +import org.json.simple.JSONObject; +import org.json.simple.parser.JSONParser; +import org.json.simple.parser.ParseException; + /** * Base class for Ensembl sequence fetchers * @@ -57,12 +62,6 @@ import java.util.List; */ public abstract class EnsemblSeqProxy extends EnsemblRestClient { - private static final String ALLELES = "alleles"; - - protected static final String PARENT = "Parent"; - - protected static final String ID = "ID"; - protected static final String NAME = "Name"; protected static final String DESCRIPTION = "description"; @@ -137,8 +136,8 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient // danger: accession separator used as a regex here, a string elsewhere // in this case it is ok (it is just a space), but (e.g.) '\' would not be - List allIds = Arrays.asList(query - .split(getAccessionSeparator())); + List allIds = Arrays + .asList(query.split(getAccessionSeparator())); AlignmentI alignment = null; inProgress = true; @@ -207,7 +206,8 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient try { /* - * get 'dummy' genomic sequence with exon, cds and variation features + * get 'dummy' genomic sequence with gene, transcript, + * exon, cds and variation features */ SequenceI genomicSequence = null; EnsemblFeatures gffFetcher = new EnsemblFeatures(getDomain()); @@ -223,7 +223,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient /* * transfer features to the query sequence */ - SequenceI querySeq = alignment.findName(accId); + SequenceI querySeq = alignment.findName(accId, true); if (transferFeatures(accId, genomicSequence, querySeq)) { @@ -236,8 +236,8 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient } } catch (IOException e) { - System.err.println("Error transferring Ensembl features: " - + e.getMessage()); + System.err.println( + "Error transferring Ensembl features: " + e.getMessage()); } } @@ -275,8 +275,8 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient proteinSeq.createDatasetSequence(); querySeq.createDatasetSequence(); - MapList mapList = AlignmentUtils - .mapCdsToProtein(querySeq, proteinSeq); + MapList mapList = AlignmentUtils.mapCdsToProtein(querySeq, + proteinSeq); if (mapList != null) { // clunky: ensure Uniprot xref if we have one is on mapped sequence @@ -287,9 +287,11 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient getEnsemblDataVersion(), proteinSeq.getName(), map); querySeq.getDatasetSequence().addDBRef(dbr); DBRefEntry[] uprots = DBRefUtils.selectRefs(ds.getDBRefs(), - new String[] { DBRefSource.UNIPROT }); + new String[] + { DBRefSource.UNIPROT }); DBRefEntry[] upxrefs = DBRefUtils.selectRefs(querySeq.getDBRefs(), - new String[] { DBRefSource.UNIPROT }); + new String[] + { DBRefSource.UNIPROT }); if (uprots != null) { for (DBRefEntry up : uprots) @@ -304,8 +306,8 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient if (upx.size() > 1) { - Cache.log - .warn("Implementation issue - multiple uniprot acc on product sequence."); + Cache.log.warn( + "Implementation issue - multiple uniprot acc on product sequence."); } } else @@ -330,8 +332,8 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient * copy exon features to protein, compute peptide variants from dna * variants and add as features on the protein sequence ta-da */ - AlignmentUtils - .computeProteinFeatures(querySeq, proteinSeq, mapList); + AlignmentUtils.computeProteinFeatures(querySeq, proteinSeq, + mapList); } } catch (Exception e) { @@ -364,8 +366,8 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient /* * and add a reference to itself */ - DBRefEntry self = new DBRefEntry(getDbSource(), - getEnsemblDataVersion(), seq.getName()); + DBRefEntry self = new DBRefEntry(getDbSource(), getEnsemblDataVersion(), + seq.getName()); seq.addDBRef(self); } @@ -379,58 +381,52 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient * @throws JalviewException * @throws IOException */ - protected AlignmentI fetchSequences(List ids, AlignmentI alignment) - throws JalviewException, IOException + protected AlignmentI fetchSequences(List ids, + AlignmentI alignment) throws JalviewException, IOException { if (!isEnsemblAvailable()) { inProgress = false; throw new JalviewException("ENSEMBL Rest API not available."); } - FileParse fp = getSequenceReader(ids); - if (fp == null) + BufferedReader br = getSequenceReader(ids); + if (br == null) { return alignment; } - FastaFile fr = new FastaFile(fp); - if (fr.hasWarningMessage()) - { - System.out.println(String.format( - "Warning when retrieving %d ids %s\n%s", ids.size(), - ids.toString(), fr.getWarningMessage())); - } - else if (fr.getSeqs().size() != ids.size()) + List seqs = parseSequenceJson(br); + + if (seqs.isEmpty()) { - System.out.println(String.format( - "Only retrieved %d sequences for %d query strings", fr - .getSeqs().size(), ids.size())); + throw new IOException("No data returned for " + ids); } - if (fr.getSeqs().size() == 1 && fr.getSeqs().get(0).getLength() == 0) + if (seqs.size() != ids.size()) { - /* - * POST request has returned an empty FASTA file e.g. for invalid id - */ - throw new IOException("No data returned for " + ids); + System.out.println(String.format( + "Only retrieved %d sequences for %d query strings", + seqs.size(), ids.size())); } - if (fr.getSeqs().size() > 0) + if (!seqs.isEmpty()) { - AlignmentI seqal = new Alignment(fr.getSeqsAsArray()); - for (SequenceI sq : seqal.getSequences()) + AlignmentI seqal = new Alignment( + seqs.toArray(new SequenceI[seqs.size()])); + for (SequenceI seq : seqs) { - if (sq.getDescription() == null) + if (seq.getDescription() == null) { - sq.setDescription(getDbName()); + seq.setDescription(getDbName()); } - String name = sq.getName(); + String name = seq.getName(); if (ids.contains(name) || ids.contains(name.replace("ENSP", "ENST"))) { - DBRefEntry dbref = DBRefUtils.parseToDbRef(sq, getDbSource(), + // TODO JAL-3077 use true accession version in dbref + DBRefEntry dbref = DBRefUtils.parseToDbRef(seq, getDbSource(), getEnsemblDataVersion(), name); - sq.addDBRef(dbref); + seq.addDBRef(dbref); } } if (alignment == null) @@ -446,6 +442,49 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient } /** + * Parses a JSON response into a list of sequences + * + * @param br + * @return + * @see http://rest.ensembl.org/documentation/info/sequence_id + */ + protected List parseSequenceJson(BufferedReader br) + { + JSONParser jp = new JSONParser(); + List result = new ArrayList<>(); + try + { + /* + * for now, assumes only one sequence returned; refactor if needed + * in future to handle a JSONArray with more than one + */ + final JSONObject val = (JSONObject) jp.parse(br); + Object s = val.get("desc"); + String desc = s == null ? null : s.toString(); + s = val.get("id"); + String id = s == null ? null : s.toString(); + s = val.get("seq"); + String seq = s == null ? null : s.toString(); + Sequence sequence = new Sequence(id, seq); + if (desc != null) + { + sequence.setDescription(desc); + } + // todo JAL-3077 make a DBRefEntry with true accession version + // s = val.get("version"); + // String version = s == null ? "0" : s.toString(); + // DBRefEntry dbref = new DBRefEntry(getDbSource(), version, id); + // sequence.addDBRef(dbref); + result.add(sequence); + } catch (ParseException | IOException e) + { + System.err.println("Error processing JSON response: " + e.toString()); + // ignore + } + return result; + } + + /** * Returns the URL for the REST call * * @return @@ -466,13 +505,31 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient } // @see https://github.com/Ensembl/ensembl-rest/wiki/Output-formats urlstring.append("?type=").append(getSourceEnsemblType().getType()); - urlstring.append(("&Accept=text/x-fasta")); + urlstring.append(("&Accept=application/json")); + urlstring.append(("&Content-Type=application/json")); + + String objectType = getObjectType(); + if (objectType != null) + { + urlstring.append("&").append(OBJECT_TYPE).append("=") + .append(objectType); + } URL url = new URL(urlstring.toString()); return url; } /** + * Override this method to specify object_type request parameter + * + * @return + */ + protected String getObjectType() + { + return null; + } + + /** * A sequence/id POST request currently allows up to 50 queries * * @see http://rest.ensembl.org/documentation/info/sequence_id_post @@ -489,18 +546,6 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient return false; } - @Override - protected String getRequestMimeType(boolean multipleIds) - { - return multipleIds ? "application/json" : "text/x-fasta"; - } - - @Override - protected String getResponseMimeType() - { - return "text/x-fasta"; - } - /** * * @return the configured sequence return type for this source @@ -536,8 +581,9 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient protected MapList getGenomicRangesFromFeatures(SequenceI sourceSequence, String accId, int start) { - SequenceFeature[] sfs = sourceSequence.getSequenceFeatures(); - if (sfs == null) + List sfs = sourceSequence.getFeatures() + .getPositionalFeatures(); + if (sfs.isEmpty()) { return null; } @@ -546,7 +592,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient * generously initial size for number of cds regions * (worst case titin Q8WZ42 has c. 313 exons) */ - List regions = new ArrayList(100); + List regions = new ArrayList<>(100); int mappedLength = 0; int direction = 1; // forward boolean directionSet = false; @@ -565,8 +611,8 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient if (directionSet && strand != direction) { // abort - mix of forward and backward - System.err.println("Error: forward and backward strand for " - + accId); + System.err.println( + "Error: forward and backward strand for " + accId); return null; } direction = strand; @@ -607,10 +653,12 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient * a final sort is needed since Ensembl returns CDS sorted within source * (havana / ensembl_havana) */ - Collections.sort(regions, new RangeComparator(direction == 1)); + Collections.sort(regions, direction == 1 ? IntRangeComparator.ASCENDING + : IntRangeComparator.DESCENDING); - List to = Arrays.asList(new int[] { start, - start + mappedLength - 1 }); + List to = Arrays + .asList(new int[] + { start, start + mappedLength - 1 }); return new MapList(regions, to, 1, 1); } @@ -638,6 +686,20 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient String accId); /** + * Answers a list of sequence features that mark positions of the genomic + * sequence feature which are within the sequence being retrieved. For + * example, an 'exon' feature whose parent is the target transcript marks the + * cdna positions of the transcript. For a gene sequence, this is trivially + * just the 'gene' feature with matching gene id. + * + * @param seq + * @param accId + * @return + */ + protected abstract List getIdentifyingFeatures( + SequenceI seq, String accId); + + /** * Transfers the sequence feature to the target sequence, locating its start * and end range based on the mapping. Features which do not overlap the * target sequence are ignored. @@ -666,16 +728,15 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient int newBegin = Math.min(mappedRange[0], mappedRange[1]); int newEnd = Math.max(mappedRange[0], mappedRange[1]); SequenceFeature copy = new SequenceFeature(sf, newBegin, newEnd, - group); + group, sf.getScore()); targetSequence.addSequenceFeature(copy); /* * for sequence_variant on reverse strand, have to convert the allele * values to their complements */ - if (!forwardStrand - && SequenceOntologyFactory.getInstance().isA(sf.getType(), - SequenceOntologyI.SEQUENCE_VARIANT)) + if (!forwardStrand && SequenceOntologyFactory.getInstance() + .isA(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT)) { reverseComplementAlleles(copy); } @@ -690,7 +751,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient */ static void reverseComplementAlleles(SequenceFeature sf) { - final String alleles = (String) sf.getValue(ALLELES); + final String alleles = (String) sf.getValue(Gff3Helper.ALLELES); if (alleles == null) { return; @@ -701,7 +762,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient reverseComplementAllele(complement, allele); } String comp = complement.toString(); - sf.setValue(ALLELES, comp); + sf.setValue(Gff3Helper.ALLELES, comp); sf.setDescription(comp); /* @@ -711,7 +772,8 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient String atts = sf.getAttributes(); if (atts != null) { - atts = atts.replace(ALLELES + "=" + alleles, ALLELES + "=" + comp); + atts = atts.replace(Gff3Helper.ALLELES + "=" + alleles, + Gff3Helper.ALLELES + "=" + comp); sf.setAttributes(atts); } } @@ -765,8 +827,9 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient return false; } - // long start = System.currentTimeMillis(); - SequenceFeature[] sfs = sourceSequence.getSequenceFeatures(); +// long start = System.currentTimeMillis(); + List sfs = sourceSequence.getFeatures() + .getPositionalFeatures(); MapList mapping = getGenomicRangesFromFeatures(sourceSequence, accessionId, targetSequence.getStart()); if (mapping == null) @@ -776,10 +839,10 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient boolean result = transferFeatures(sfs, targetSequence, mapping, accessionId); - // System.out.println("transferFeatures (" + (sfs.length) + " --> " - // + targetSequence.getSequenceFeatures().length + ") to " - // + targetSequence.getName() - // + " took " + (System.currentTimeMillis() - start) + "ms"); +// System.out.println("transferFeatures (" + (sfs.size()) + " --> " +// + targetSequence.getFeatures().getFeatureCount(true) + ") to " +// + targetSequence.getName() + " took " +// + (System.currentTimeMillis() - start) + "ms"); return result; } @@ -788,13 +851,13 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient * converted using the mapping. Features which do not overlap are ignored. * Features whose parent is not the specified identifier are also ignored. * - * @param features + * @param sfs * @param targetSequence * @param mapping * @param parentId * @return */ - protected boolean transferFeatures(SequenceFeature[] features, + protected boolean transferFeatures(List sfs, SequenceI targetSequence, MapList mapping, String parentId) { final boolean forwardStrand = mapping.isFromForwardStrand(); @@ -804,10 +867,10 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient * position descending if reverse strand) so as to add them in * 'forwards' order to the target sequence */ - sortFeatures(features, forwardStrand); + SequenceFeatures.sortFeatures(sfs, forwardStrand); boolean transferred = false; - for (SequenceFeature sf : features) + for (SequenceFeature sf : sfs) { if (retainFeature(sf, parentId)) { @@ -819,33 +882,6 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient } /** - * Sort features by start position ascending (if on forward strand), or end - * position descending (if on reverse strand) - * - * @param features - * @param forwardStrand - */ - protected static void sortFeatures(SequenceFeature[] features, - final boolean forwardStrand) - { - Arrays.sort(features, new Comparator() - { - @Override - public int compare(SequenceFeature o1, SequenceFeature o2) - { - if (forwardStrand) - { - return Integer.compare(o1.getBegin(), o2.getBegin()); - } - else - { - return Integer.compare(o2.getEnd(), o1.getEnd()); - } - } - }); - } - - /** * Answers true if the feature type is one we want to keep for the sequence. * Some features are only retrieved in order to identify the sequence range, * and may then be discarded as redundant information (e.g. "CDS" feature for @@ -870,7 +906,8 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient { String parent = (String) sf.getValue(PARENT); // using contains to allow for prefix "gene:", "transcript:" etc - if (parent != null && !parent.contains(identifier)) + if (parent != null + && !parent.toUpperCase().contains(identifier.toUpperCase())) { // this genomic feature belongs to a different transcript return false; @@ -887,35 +924,30 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient /** * Returns a (possibly empty) list of features on the sequence which have the - * specified sequence ontology type (or a sub-type of it), and the given + * specified sequence ontology term (or a sub-type of it), and the given * identifier as parent * * @param sequence - * @param type + * @param term * @param parentId * @return */ protected List findFeatures(SequenceI sequence, - String type, String parentId) + String term, String parentId) { - List result = new ArrayList(); + List result = new ArrayList<>(); - SequenceFeature[] sfs = sequence.getSequenceFeatures(); - if (sfs != null) + List sfs = sequence.getFeatures() + .getFeaturesByOntology(term); + for (SequenceFeature sf : sfs) { - SequenceOntologyI so = SequenceOntologyFactory.getInstance(); - for (SequenceFeature sf : sfs) + String parent = (String) sf.getValue(PARENT); + if (parent != null && parent.equalsIgnoreCase(parentId)) { - if (so.isA(sf.getType(), type)) - { - String parent = (String) sf.getValue(PARENT); - if (parent.equals(parentId)) - { - result.add(sf); - } - } + result.add(sf); } } + return result; }