+/*
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.ext.ensembl;
+import jalview.analysis.AlignmentUtils;
+import jalview.analysis.Dna;
+import jalview.bin.Cache;
+import jalview.datamodel.Alignment;
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.ext.ensembl.SeqFetcher.EnsemblSeqType;
-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.ws.seqfetcher.DbSourceProxy;
-import jalview.ws.seqfetcher.DbSourceProxyImpl;
+import jalview.util.IntRangeComparator;
+import jalview.util.MapList;
+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.List;
-import com.stevesoft.pat.Regex;
+import org.json.simple.JSONObject;
+import org.json.simple.parser.JSONParser;
+import org.json.simple.parser.ParseException;
-public abstract class EnsemblSeqProxy extends DbSourceProxyImpl implements
- DbSourceProxy
+/**
+ * Base class for Ensembl sequence fetchers
+ *
+ * @see http://rest.ensembl.org/documentation/info/sequence_id
+ * @author gmcarstairs
+ */
+public abstract class EnsemblSeqProxy extends EnsemblRestClient
{
- SeqFetcher sf;
+ protected static final String DESCRIPTION = "description";
- public EnsemblSeqProxy() throws Exception
+ /*
+ * enum for 'type' parameter to the /sequence REST service
+ */
+ public enum EnsemblSeqType
{
- sf = new SeqFetcher();
- addDbSourceProperty(DBRefSource.MULTIACC);
- addDbSourceProperty(DBRefSource.SEQDB);
- // decide whether these need to be filtered according to return type
- addDbSourceProperty(DBRefSource.PROTSEQDB);
- addDbSourceProperty(DBRefSource.DNACODINGSEQDB);
- addDbSourceProperty(DBRefSource.DNASEQDB);
- }
+ /**
+ * type=genomic to fetch full dna including introns
+ */
+ GENOMIC("genomic"),
- @Override
- public String getDbSource()
- {
- return "ENSEMBL";
- }
+ /**
+ * type=cdna to fetch coding dna including UTRs
+ */
+ CDNA("cdna"),
+ /**
+ * type=cds to fetch coding dna excluding UTRs
+ */
+ CDS("cds"),
+
+ /**
+ * type=protein to fetch peptide product sequence
+ */
+ PROTEIN("protein");
+
+ /*
+ * the value of the 'type' parameter to fetch this version of
+ * an Ensembl sequence
+ */
+ private String type;
+
+ EnsemblSeqType(String t)
+ {
+ type = t;
+ }
+
+ public String getType()
+ {
+ return type;
+ }
- @Override
- public String getDbVersion()
- {
- return "0"; // sf.getVersion();
}
- @Override
- public String getAccessionSeparator()
+ /**
+ * Default constructor (to use rest.ensembl.org)
+ */
+ public EnsemblSeqProxy()
{
- return " ";
+ super();
}
- @Override
- public Regex getAccessionValidator()
+ /**
+ * Constructor given the target domain to fetch data from
+ */
+ public EnsemblSeqProxy(String d)
{
- return new Regex("((ENSP|ENST|ENSG|CCDS)[0-9.]{3,})");
+ super(d);
}
+ /**
+ * Makes the sequence queries to Ensembl's REST service and returns an
+ * alignment consisting of the returned sequences.
+ */
@Override
- public String getTestQuery()
+ public AlignmentI getSequenceRecords(String query) throws Exception
{
- return "ENSP00000288602";
+ // TODO use a String... query vararg instead?
+
+ // 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<String> allIds = Arrays
+ .asList(query.split(getAccessionSeparator()));
+ AlignmentI alignment = null;
+ inProgress = true;
+
+ /*
+ * execute queries, if necessary in batches of the
+ * maximum allowed number of ids
+ */
+ int maxQueryCount = getMaximumQueryCount();
+ for (int v = 0, vSize = allIds.size(); v < vSize; v += maxQueryCount)
+ {
+ int p = Math.min(vSize, v + maxQueryCount);
+ List<String> ids = allIds.subList(v, p);
+ try
+ {
+ alignment = fetchSequences(ids, alignment);
+ } catch (Throwable r)
+ {
+ inProgress = false;
+ String msg = "Aborting ID retrieval after " + v
+ + " chunks. Unexpected problem (" + r.getLocalizedMessage()
+ + ")";
+ System.err.println(msg);
+ r.printStackTrace();
+ break;
+ }
+ }
+
+ if (alignment == null)
+ {
+ return null;
+ }
+
+ /*
+ * fetch and transfer genomic sequence features,
+ * fetch protein product and add as cross-reference
+ */
+ for (String accId : allIds)
+ {
+ addFeaturesAndProduct(accId, alignment);
+ }
+
+ for (SequenceI seq : alignment.getSequences())
+ {
+ getCrossReferences(seq);
+ }
+
+ return alignment;
}
- @Override
- public boolean isValidReference(String accession)
+ /**
+ * Fetches Ensembl features using the /overlap REST endpoint, and adds them to
+ * the sequence in the alignment. Also fetches the protein product, maps it
+ * from the CDS features of the sequence, and saves it as a cross-reference of
+ * the dna sequence.
+ *
+ * @param accId
+ * @param alignment
+ */
+ protected void addFeaturesAndProduct(String accId, AlignmentI alignment)
{
- return getAccessionValidator().search(accession);
+ if (alignment == null)
+ {
+ return;
+ }
+
+ try
+ {
+ /*
+ * get 'dummy' genomic sequence with gene, transcript,
+ * exon, cds and variation features
+ */
+ SequenceI genomicSequence = null;
+ EnsemblFeatures gffFetcher = new EnsemblFeatures(getDomain());
+ EnsemblFeatureType[] features = getFeaturesToFetch();
+ AlignmentI geneFeatures = gffFetcher.getSequenceRecords(accId,
+ features);
+ if (geneFeatures != null && geneFeatures.getHeight() > 0)
+ {
+ genomicSequence = geneFeatures.getSequenceAt(0);
+ }
+ if (genomicSequence != null)
+ {
+ /*
+ * transfer features to the query sequence
+ */
+ SequenceI querySeq = alignment.findName(accId, true);
+ if (transferFeatures(accId, genomicSequence, querySeq))
+ {
+
+ /*
+ * fetch and map protein product, and add it as a cross-reference
+ * of the retrieved sequence
+ */
+ addProteinProduct(querySeq);
+ }
+ }
+ } catch (IOException e)
+ {
+ System.err.println(
+ "Error transferring Ensembl features: " + e.getMessage());
+ }
}
- private volatile boolean inProgress = false;
+ /**
+ * Returns those sequence feature types to fetch from Ensembl. We may want
+ * features either because they are of interest to the user, or as means to
+ * identify the locations of the sequence on the genomic sequence (CDS
+ * features identify CDS, exon features identify cDNA etc).
+ *
+ * @return
+ */
+ protected abstract EnsemblFeatureType[] getFeaturesToFetch();
- @Override
- public AlignmentI getSequenceRecords(String queries) throws Exception
+ /**
+ * Fetches and maps the protein product, and adds it as a cross-reference of
+ * the retrieved sequence
+ */
+ protected void addProteinProduct(SequenceI querySeq)
{
- inProgress = true;
- List<String> tids, ids = new ArrayList<String>();
- tids = Arrays.asList(queries.split(" +"));
- AlignmentI rtn = null;
- for (int v = 0, vSize = tids.size(); v < vSize; v += 50)
+ String accId = querySeq.getName();
+ try
{
- int p = v + 50;
- if (p > vSize)
+ AlignmentI protein = new EnsemblProtein(getDomain())
+ .getSequenceRecords(accId);
+ if (protein == null || protein.getHeight() == 0)
{
- p = vSize;
+ System.out.println("No protein product found for " + accId);
+ return;
}
- ;
- ids = tids.subList(v, p);
- try
+ SequenceI proteinSeq = protein.getSequenceAt(0);
+
+ /*
+ * need dataset sequences (to be the subject of mappings)
+ */
+ proteinSeq.createDatasetSequence();
+ querySeq.createDatasetSequence();
+
+ MapList mapList = AlignmentUtils.mapCdsToProtein(querySeq,
+ proteinSeq);
+ if (mapList != null)
{
- if (!sf.isEnsemblAvailable())
- {
- inProgress = false;
- throw new JalviewException("ENSEMBL Rest API not available.");
- }
- FileParse fp = new FileParse(sf.getSequenceReader(
- getSourceEnsemblType(), ids));
- FastaFile fr = new FastaFile(fp);
- if (fr.hasWarningMessage())
- {
- System.out
- .println("Warning when retrieving " + ids.size() + " ids"
- + ids.toString() + "\n" + fr.getWarningMessage());
- }
- else if (fr.getSeqs().size() != ids.size())
+ // clunky: ensure Uniprot xref if we have one is on mapped sequence
+ SequenceI ds = proteinSeq.getDatasetSequence();
+ // TODO: Verify ensp primary ref is on proteinSeq.getDatasetSequence()
+ Mapping map = new Mapping(ds, mapList);
+ DBRefEntry dbr = new DBRefEntry(getDbSource(),
+ getEnsemblDataVersion(), proteinSeq.getName(), map);
+ querySeq.getDatasetSequence().addDBRef(dbr);
+ DBRefEntry[] uprots = DBRefUtils.selectRefs(ds.getDBRefs(),
+ new String[]
+ { DBRefSource.UNIPROT });
+ DBRefEntry[] upxrefs = DBRefUtils.selectRefs(querySeq.getDBRefs(),
+ new String[]
+ { DBRefSource.UNIPROT });
+ if (uprots != null)
{
- System.out.println("Only retrieved " + fr.getSeqs().size()
- + " sequences for " + ids.size() + " query strings.");
- }
- if (fr.getSeqs().size() > 0)
- {
- AlignmentI seqal = new jalview.datamodel.Alignment(
- fr.getSeqsAsArray());
- for (SequenceI sq:seqal.getSequences())
+ for (DBRefEntry up : uprots)
{
- if (ids.contains((sq.getName())))
+ // locate local uniprot ref and map
+ List<DBRefEntry> upx = DBRefUtils.searchRefs(upxrefs,
+ up.getAccessionId());
+ DBRefEntry upxref;
+ if (upx.size() != 0)
{
- DBRefUtils.parseToDbRef(sq, "ENSEMBL", "0", sq.getName());
+ upxref = upx.get(0);
+
+ if (upx.size() > 1)
+ {
+ Cache.log.warn(
+ "Implementation issue - multiple uniprot acc on product sequence.");
+ }
}
- }
- if (rtn == null)
- {
- rtn = seqal;
- }
- else
- {
- rtn.append(seqal);
+ else
+ {
+ upxref = new DBRefEntry(DBRefSource.UNIPROT,
+ getEnsemblDataVersion(), up.getAccessionId());
+ }
+
+ Mapping newMap = new Mapping(ds, mapList);
+ upxref.setVersion(getEnsemblDataVersion());
+ upxref.setMap(newMap);
+ if (upx.size() == 0)
+ {
+ // add the new uniprot ref
+ querySeq.getDatasetSequence().addDBRef(upxref);
+ }
+
}
}
- } catch (Throwable r)
+
+ /*
+ * 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);
+ }
+ } catch (Exception e)
+ {
+ System.err
+ .println(String.format("Error retrieving protein for %s: %s",
+ accId, e.getMessage()));
+ }
+ }
+
+ /**
+ * Get database xrefs from Ensembl, and attach them to the sequence
+ *
+ * @param seq
+ */
+ protected void getCrossReferences(SequenceI seq)
+ {
+ while (seq.getDatasetSequence() != null)
+ {
+ seq = seq.getDatasetSequence();
+ }
+
+ EnsemblXref xrefFetcher = new EnsemblXref(getDomain(), getDbSource(),
+ getEnsemblDataVersion());
+ List<DBRefEntry> xrefs = xrefFetcher.getCrossReferences(seq.getName());
+ for (DBRefEntry xref : xrefs)
+ {
+ seq.addDBRef(xref);
+ }
+
+ /*
+ * and add a reference to itself
+ */
+ DBRefEntry self = new DBRefEntry(getDbSource(), getEnsemblDataVersion(),
+ seq.getName());
+ seq.addDBRef(self);
+ }
+
+ /**
+ * Fetches sequences for the list of accession ids and adds them to the
+ * alignment. Returns the extended (or created) alignment.
+ *
+ * @param ids
+ * @param alignment
+ * @return
+ * @throws JalviewException
+ * @throws IOException
+ */
+ protected AlignmentI fetchSequences(List<String> ids,
+ AlignmentI alignment) throws JalviewException, IOException
+ {
+ if (!isEnsemblAvailable())
+ {
+ inProgress = false;
+ throw new JalviewException("ENSEMBL Rest API not available.");
+ }
+ BufferedReader br = getSequenceReader(ids);
+ if (br == null)
+ {
+ return alignment;
+ }
+
+ List<SequenceI> seqs = parseSequenceJson(br);
+
+ if (seqs.isEmpty())
+ {
+ throw new IOException("No data returned for " + ids);
+ }
+
+ if (seqs.size() != ids.size())
+ {
+ System.out.println(String.format(
+ "Only retrieved %d sequences for %d query strings",
+ seqs.size(), ids.size()));
+ }
+
+ if (!seqs.isEmpty())
+ {
+ AlignmentI seqal = new Alignment(
+ seqs.toArray(new SequenceI[seqs.size()]));
+ for (SequenceI seq : seqs)
{
- inProgress = false;
- if (rtn != null)
+ if (seq.getDescription() == null)
{
- System.err.println("Aborting ID retrieval after " + v
- + " chunks.");
- r.printStackTrace();
+ seq.setDescription(getDbName());
}
- else
+ String name = seq.getName();
+ if (ids.contains(name)
+ || ids.contains(name.replace("ENSP", "ENST")))
{
-
- throw new JalviewException("Aborting ID retrieval after " + v
- + " chunks. Unexpected problem ("
- + r.getLocalizedMessage() + ")", r);
+ // TODO JAL-3077 use true accession version in dbref
+ DBRefEntry dbref = DBRefUtils.parseToDbRef(seq, getDbSource(),
+ getEnsemblDataVersion(), name);
+ seq.addDBRef(dbref);
}
+ }
+ if (alignment == null)
+ {
+ alignment = seqal;
+ }
+ else
+ {
+ alignment.append(seqal);
+ }
+ }
+ return alignment;
+ }
+ /**
+ * 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<SequenceI> parseSequenceJson(BufferedReader br)
+ {
+ JSONParser jp = new JSONParser();
+ List<SequenceI> 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
}
- inProgress = false;
- return rtn;
+ return result;
}
/**
+ * Returns the URL for the REST call
*
- * @return the configured sequence return type for this source
+ * @return
+ * @throws MalformedURLException
*/
- protected abstract EnsemblSeqType getSourceEnsemblType();
+ @Override
+ protected URL getUrl(List<String> ids) throws MalformedURLException
+ {
+ /*
+ * a single id is included in the URL path
+ * multiple ids go in the POST body instead
+ */
+ StringBuffer urlstring = new StringBuffer(128);
+ urlstring.append(getDomain() + "/sequence/id");
+ if (ids.size() == 1)
+ {
+ urlstring.append("/").append(ids.get(0));
+ }
+ // @see https://github.com/Ensembl/ensembl-rest/wiki/Output-formats
+ urlstring.append("?type=").append(getSourceEnsemblType().getType());
+ 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
+ */
@Override
- public boolean queryInProgress()
+ public int getMaximumQueryCount()
{
- return inProgress;
+ return 50;
}
@Override
- public StringBuffer getRawRecords()
+ protected boolean useGetRequest()
{
- return null;
+ return false;
}
+ /**
+ *
+ * @return the configured sequence return type for this source
+ */
+ protected abstract EnsemblSeqType getSourceEnsemblType();
+
+ /**
+ * Returns a list of [start, end] genomic ranges corresponding to the sequence
+ * being retrieved.
+ *
+ * The correspondence between the frames of reference is made by locating
+ * those features on the genomic sequence which identify the retrieved
+ * sequence. Specifically
+ * <ul>
+ * <li>genomic sequence is identified by "transcript" features with
+ * ID=transcript:transcriptId</li>
+ * <li>cdna sequence is identified by "exon" features with
+ * Parent=transcript:transcriptId</li>
+ * <li>cds sequence is identified by "CDS" features with
+ * Parent=transcript:transcriptId</li>
+ * </ul>
+ *
+ * The returned ranges are sorted to run forwards (for positive strand) or
+ * backwards (for negative strand). Aborts and returns null if both positive
+ * and negative strand are found (this should not normally happen).
+ *
+ * @param sourceSequence
+ * @param accId
+ * @param start
+ * the start position of the sequence we are mapping to
+ * @return
+ */
+ protected MapList getGenomicRangesFromFeatures(SequenceI sourceSequence,
+ String accId, int start)
+ {
+ List<SequenceFeature> sfs = getIdentifyingFeatures(sourceSequence,
+ accId);
+ if (sfs.isEmpty())
+ {
+ return null;
+ }
+
+ /*
+ * generously initial size for number of cds regions
+ * (worst case titin Q8WZ42 has c. 313 exons)
+ */
+ List<int[]> 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;
+
+ /*
+ * 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 (regions.isEmpty())
+ {
+ System.out.println("Failed to identify target sequence for " + accId
+ + " from genomic features");
+ return null;
+ }
+
+ /*
+ * a final sort is needed since Ensembl returns CDS sorted within source
+ * (havana / ensembl_havana)
+ */
+ Collections.sort(regions, direction == 1 ? IntRangeComparator.ASCENDING
+ : IntRangeComparator.DESCENDING);
+
+ List<int[]> to = Arrays
+ .asList(new int[]
+ { start, start + mappedLength - 1 });
+
+ return new MapList(regions, to, 1, 1);
+ }
+
+ /**
+ * 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<SequenceFeature> 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.
+ *
+ * @param sf
+ * @param targetSequence
+ * @param mapping
+ * mapping from the sequence feature's coordinates to the target
+ * sequence
+ * @param forwardStrand
+ */
+ protected void transferFeature(SequenceFeature sf,
+ SequenceI targetSequence, MapList mapping, boolean forwardStrand)
+ {
+ int start = sf.getBegin();
+ int end = sf.getEnd();
+ int[] mappedRange = mapping.locateInTo(start, end);
+
+ if (mappedRange != null)
+ {
+ String group = sf.getFeatureGroup();
+ if (".".equals(group))
+ {
+ group = getDbSource();
+ }
+ int newBegin = Math.min(mappedRange[0], mappedRange[1]);
+ int newEnd = Math.max(mappedRange[0], mappedRange[1]);
+ SequenceFeature copy = new SequenceFeature(sf, newBegin, newEnd,
+ 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))
+ {
+ reverseComplementAlleles(copy);
+ }
+ }
+ }
+
+ /**
+ * Change the 'alleles' value of a feature by converting to complementary
+ * bases, and also update the feature description to match
+ *
+ * @param sf
+ */
+ static void reverseComplementAlleles(SequenceFeature sf)
+ {
+ final String alleles = (String) sf.getValue(Gff3Helper.ALLELES);
+ if (alleles == null)
+ {
+ return;
+ }
+ StringBuilder complement = new StringBuilder(alleles.length());
+ for (String allele : alleles.split(","))
+ {
+ reverseComplementAllele(complement, allele);
+ }
+ String comp = complement.toString();
+ sf.setValue(Gff3Helper.ALLELES, comp);
+ sf.setDescription(comp);
+
+ /*
+ * replace value of "alleles=" in sf.ATTRIBUTES as well
+ * so 'output as GFF' shows reverse complement alleles
+ */
+ String atts = sf.getAttributes();
+ if (atts != null)
+ {
+ atts = atts.replace(Gff3Helper.ALLELES + "=" + alleles,
+ Gff3Helper.ALLELES + "=" + comp);
+ sf.setAttributes(atts);
+ }
+ }
+
+ /**
+ * Makes the 'reverse complement' of the given allele and appends it to the
+ * buffer, after a comma separator if not the first
+ *
+ * @param complement
+ * @param allele
+ */
+ static void reverseComplementAllele(StringBuilder complement,
+ String allele)
+ {
+ if (complement.length() > 0)
+ {
+ complement.append(",");
+ }
+
+ /*
+ * some 'alleles' are actually descriptive terms
+ * e.g. HGMD_MUTATION, PhenCode_variation
+ * - we don't want to 'reverse complement' these
+ */
+ if (!Comparison.isNucleotideSequence(allele, true))
+ {
+ complement.append(allele);
+ }
+ else
+ {
+ for (int i = allele.length() - 1; i >= 0; i--)
+ {
+ complement.append(Dna.getComplement(allele.charAt(i)));
+ }
+ }
+ }
+
+ /**
+ * Transfers features from sourceSequence to targetSequence
+ *
+ * @param accessionId
+ * @param sourceSequence
+ * @param targetSequence
+ * @return true if any features were transferred, else false
+ */
+ protected boolean transferFeatures(String accessionId,
+ SequenceI sourceSequence, SequenceI targetSequence)
+ {
+ if (sourceSequence == null || targetSequence == null)
+ {
+ return false;
+ }
+
+// long start = System.currentTimeMillis();
+ List<SequenceFeature> sfs = sourceSequence.getFeatures()
+ .getPositionalFeatures();
+ MapList mapping = getGenomicRangesFromFeatures(sourceSequence,
+ accessionId, targetSequence.getStart());
+ if (mapping == null)
+ {
+ return false;
+ }
+
+ boolean result = transferFeatures(sfs, targetSequence, mapping,
+ accessionId);
+// System.out.println("transferFeatures (" + (sfs.size()) + " --> "
+// + targetSequence.getFeatures().getFeatureCount(true) + ") to "
+// + targetSequence.getName() + " took "
+// + (System.currentTimeMillis() - start) + "ms");
+ return result;
+ }
+
+ /**
+ * Transfer features to the target sequence. The start/end positions are
+ * converted using the mapping. Features which do not overlap are ignored.
+ * Features whose parent is not the specified identifier are also ignored.
+ *
+ * @param sfs
+ * @param targetSequence
+ * @param mapping
+ * @param parentId
+ * @return
+ */
+ protected boolean transferFeatures(List<SequenceFeature> sfs,
+ SequenceI targetSequence, MapList mapping, String parentId)
+ {
+ final boolean forwardStrand = mapping.isFromForwardStrand();
+
+ /*
+ * sort features by start position (which corresponds to end
+ * position descending if reverse strand) so as to add them in
+ * 'forwards' order to the target sequence
+ */
+ SequenceFeatures.sortFeatures(sfs, forwardStrand);
+
+ boolean transferred = false;
+ for (SequenceFeature sf : sfs)
+ {
+ if (retainFeature(sf, parentId))
+ {
+ transferFeature(sf, targetSequence, mapping, forwardStrand);
+ transferred = true;
+ }
+ }
+ return transferred;
+ }
+
+ /**
+ * 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
+ * a CDS sequence).
+ */
+ @SuppressWarnings("unused")
+ protected boolean retainFeature(SequenceFeature sf, String accessionId)
+ {
+ return true; // override as required
+ }
+
+ /**
+ * Answers true if the feature has a Parent which refers to the given
+ * accession id, or if the feature has no parent. Answers false if the
+ * feature's Parent is for a different accession id.
+ *
+ * @param sf
+ * @param identifier
+ * @return
+ */
+ protected boolean featureMayBelong(SequenceFeature sf, String identifier)
+ {
+ String parent = (String) sf.getValue(PARENT);
+ if (parent != null
+ && !parent.equalsIgnoreCase(identifier))
+ {
+ // this genomic feature belongs to a different transcript
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ * Answers a short description of the sequence fetcher
+ */
@Override
- public int getTier()
+ public String getDescription()
+ {
+ return "Ensembl " + getSourceEnsemblType().getType()
+ + " sequence with variant features";
+ }
+
+ /**
+ * Returns a (possibly empty) list of features on the sequence which have the
+ * specified sequence ontology term (or a sub-type of it), and the given
+ * identifier as parent
+ *
+ * @param sequence
+ * @param term
+ * @param parentId
+ * @return
+ */
+ protected List<SequenceFeature> findFeatures(SequenceI sequence,
+ String term, String parentId)
+ {
+ List<SequenceFeature> result = new ArrayList<>();
+
+ List<SequenceFeature> sfs = sequence.getFeatures()
+ .getFeaturesByOntology(term);
+ for (SequenceFeature sf : sfs)
+ {
+ String parent = (String) sf.getValue(PARENT);
+ if (parent != null && parent.equalsIgnoreCase(parentId))
+ {
+ result.add(sf);
+ }
+ }
+
+ return result;
+ }
+
+ /**
+ * Answers true if the feature type is either 'NMD_transcript_variant' or
+ * 'transcript' (or one of its sub-types in the Sequence Ontology). This is
+ * because NMD_transcript_variant behaves like 'transcript' in Ensembl
+ * although strictly speaking it is not (it is a sub-type of
+ * sequence_variant).
+ * <p>
+ * (This test was needed when fetching transcript features as GFF. As we are
+ * now fetching as JSON, all features have type 'transcript' so the check for
+ * NMD_transcript_variant is redundant. Left in for any future case arising.)
+ *
+ * @param featureType
+ * @return
+ */
+ public static boolean isTranscript(String featureType)
{
- return 0;
+ return SequenceOntologyI.NMD_TRANSCRIPT_VARIANT.equals(featureType)
+ || SequenceOntologyFactory.getInstance().isA(featureType,
+ SequenceOntologyI.TRANSCRIPT);
}
}
git://source.jalview.org / jalview.git / blobdiff