X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblSeqProxy.java;h=7b448fd8a6389becba113ec2e2b40d6bb997b959;hb=ef84f77ebe6c73e67e8ec789b02f41891715ebdd;hp=35ceea338680bb98b2cf7584ae796824d718ecf5;hpb=55eef00ac2435b5cc0ee64b92ad87a915375a709;p=jalview.git diff --git a/src/jalview/ext/ensembl/EnsemblSeqProxy.java b/src/jalview/ext/ensembl/EnsemblSeqProxy.java index 35ceea3..7b448fd 100644 --- a/src/jalview/ext/ensembl/EnsemblSeqProxy.java +++ b/src/jalview/ext/ensembl/EnsemblSeqProxy.java @@ -28,12 +28,11 @@ 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; @@ -42,6 +41,7 @@ import jalview.util.DBRefUtils; import jalview.util.IntRangeComparator; import jalview.util.MapList; +import java.io.BufferedReader; import java.io.IOException; import java.net.MalformedURLException; import java.net.URL; @@ -49,8 +49,10 @@ import java.util.ArrayList; import java.util.Arrays; import java.util.Collections; import java.util.List; -import java.util.Map; -import java.util.Map.Entry; + +import org.json.simple.JSONObject; +import org.json.simple.parser.JSONParser; +import org.json.simple.parser.ParseException; /** * Base class for Ensembl sequence fetchers @@ -60,10 +62,6 @@ import java.util.Map.Entry; */ public abstract class EnsemblSeqProxy extends EnsemblRestClient { - protected static final String PARENT = "Parent"; - - protected static final String ID = "ID"; - protected static final String NAME = "Name"; protected static final String DESCRIPTION = "description"; @@ -208,7 +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()); @@ -224,7 +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)) { @@ -390,50 +389,44 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient 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()) + List seqs = parseSequenceJson(br); + + if (seqs.isEmpty()) { - System.out.println( - String.format("Warning when retrieving %d ids %s\n%s", - ids.size(), ids.toString(), fr.getWarningMessage())); + throw new IOException("No data returned for " + ids); } - else if (fr.getSeqs().size() != ids.size()) + + if (seqs.size() != ids.size()) { System.out.println(String.format( "Only retrieved %d sequences for %d query strings", - fr.getSeqs().size(), ids.size())); - } - - if (fr.getSeqs().size() == 1 && fr.getSeqs().get(0).getLength() == 0) - { - /* - * POST request has returned an empty FASTA file e.g. for invalid id - */ - throw new IOException("No data returned for " + ids); + 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) @@ -449,6 +442,49 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient } /** + * Parses a JSON response for a single sequence ID query + * + * @param br + * @return a single jalview.datamodel.Sequence + * @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 @@ -469,16 +505,14 @@ 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")); - Map params = getAdditionalParameters(); - if (params != null) + String objectType = getObjectType(); + if (objectType != null) { - for (Entry entry : params.entrySet()) - { - urlstring.append("&").append(entry.getKey()).append("=") - .append(entry.getValue()); - } + urlstring.append("&").append(OBJECT_TYPE).append("=") + .append(objectType); } URL url = new URL(urlstring.toString()); @@ -486,11 +520,11 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient } /** - * Override this method to add any additional x=y URL parameters needed + * Override this method to specify object_type request parameter * * @return */ - protected Map getAdditionalParameters() + protected String getObjectType() { return null; } @@ -512,18 +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 @@ -559,9 +581,8 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient protected MapList getGenomicRangesFromFeatures(SequenceI sourceSequence, String accId, int start) { - // SequenceFeature[] sfs = sourceSequence.getSequenceFeatures(); - List sfs = sourceSequence.getFeatures() - .getPositionalFeatures(); + List sfs = getIdentifyingFeatures(sourceSequence, + accId); if (sfs.isEmpty()) { return null; @@ -571,54 +592,38 @@ 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; for (SequenceFeature sf : sfs) { + int strand = sf.getStrand(); + strand = strand == 0 ? 1 : strand; // treat unknown as forward + + if (directionSet && strand != direction) + { + // abort - mix of forward and backward + System.err + .println("Error: forward and backward strand for " + accId); + return null; + } + direction = strand; + directionSet = true; + /* - * accept the target feature type or a specialisation of it - * (e.g. coding_exon for exon) + * add to CDS ranges, semi-sorted forwards/backwards */ - if (identifiesSequence(sf, accId)) + if (strand < 0) { - int strand = sf.getStrand(); - strand = strand == 0 ? 1 : strand; // treat unknown as forward - - if (directionSet && strand != direction) - { - // abort - mix of forward and backward - System.err.println( - "Error: forward and backward strand for " + accId); - return null; - } - direction = strand; - directionSet = true; - - /* - * add to CDS ranges, semi-sorted forwards/backwards - */ - if (strand < 0) - { - regions.add(0, new int[] { sf.getEnd(), sf.getBegin() }); - } - else - { - regions.add(new int[] { sf.getBegin(), sf.getEnd() }); - } - mappedLength += Math.abs(sf.getEnd() - sf.getBegin() + 1); - - if (!isSpliceable()) - { - /* - * 'gene' sequence is contiguous so we can stop as soon as its - * identifying feature has been found - */ - break; - } + regions.add(0, new int[] { sf.getEnd(), sf.getBegin() }); + } + else + { + regions.add(new int[] { sf.getBegin(), sf.getEnd() }); } + mappedLength += Math.abs(sf.getEnd() - sf.getBegin() + 1); } if (regions.isEmpty()) @@ -643,26 +648,18 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient } /** - * Answers true if the sequence being retrieved may occupy discontiguous - * regions on the genomic sequence. - */ - protected boolean isSpliceable() - { - return true; - } - - /** - * Returns true if the sequence feature marks positions of the genomic + * 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. + * cdna positions of the transcript. For a gene sequence, this is trivially + * just the 'gene' feature with matching gene id. * - * @param sf + * @param seq * @param accId * @return */ - protected abstract boolean identifiesSequence(SequenceFeature sf, - String accId); + protected abstract List getIdentifyingFeatures( + SequenceI seq, String accId); /** * Transfers the sequence feature to the target sequence, locating its start @@ -871,7 +868,8 @@ 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; @@ -899,14 +897,14 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient protected List findFeatures(SequenceI sequence, String term, String parentId) { - List result = new ArrayList(); + List result = new ArrayList<>(); List sfs = sequence.getFeatures() .getFeaturesByOntology(term); for (SequenceFeature sf : sfs) { String parent = (String) sf.getValue(PARENT); - if (parent != null && parent.equals(parentId)) + if (parent != null && parent.equalsIgnoreCase(parentId)) { result.add(sf); }