X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblSeqProxy.java;h=7b448fd8a6389becba113ec2e2b40d6bb997b959;hb=ef84f77ebe6c73e67e8ec789b02f41891715ebdd;hp=e986ba832d7994e38bab3469f25a48262389ef26;hpb=b03ec66ae6238b44bd20d2403d1157cadc5f0e01;p=jalview.git
diff --git a/src/jalview/ext/ensembl/EnsemblSeqProxy.java b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
index e986ba8..7b448fd 100644
--- a/src/jalview/ext/ensembl/EnsemblSeqProxy.java
+++ b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
@@ -1,54 +1,93 @@
+/*
+ * 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.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.io.FastaFile;
-import jalview.io.FileParse;
-import jalview.io.gff.SequenceOntology;
+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 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
*
+ * @see http://rest.ensembl.org/documentation/info/sequence_id
* @author gmcarstairs
*/
public abstract class EnsemblSeqProxy extends EnsemblRestClient
{
+ protected static final String NAME = "Name";
+
+ protected static final String DESCRIPTION = "description";
+
+ /*
+ * enum for 'type' parameter to the /sequence REST service
+ */
public enum EnsemblSeqType
{
/**
- * type=genomic for the full dna including introns
+ * type=genomic to fetch full dna including introns
*/
GENOMIC("genomic"),
/**
- * type=cdna for transcribed dna including UTRs
+ * type=cdna to fetch coding dna including UTRs
*/
CDNA("cdna"),
/**
- * type=cds for coding dna excluding UTRs
+ * type=cds to fetch coding dna excluding UTRs
*/
CDS("cds"),
/**
- * type=protein for the peptide product sequence
+ * type=protein to fetch peptide product sequence
*/
PROTEIN("protein");
@@ -71,35 +110,24 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
}
/**
- * A comparator to sort ranges into ascending start position order
+ * Default constructor (to use rest.ensembl.org)
*/
- private class RangeSorter implements Comparator
+ public EnsemblSeqProxy()
{
- boolean forwards;
-
- RangeSorter(boolean forward)
- {
- forwards = forward;
- }
-
- @Override
- public int compare(int[] o1, int[] o2)
- {
- return (forwards ? 1 : -1) * Integer.compare(o1[0], o2[0]);
- }
-
- };
+ super();
+ }
/**
- * Constructor
+ * Constructor given the target domain to fetch data from
*/
- public EnsemblSeqProxy()
+ public EnsemblSeqProxy(String d)
{
+ super(d);
}
/**
* Makes the sequence queries to Ensembl's REST service and returns an
- * alignment consisting of the returned sequences
+ * alignment consisting of the returned sequences.
*/
@Override
public AlignmentI getSequenceRecords(String query) throws Exception
@@ -108,7 +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;
@@ -131,26 +160,30 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
+ " chunks. Unexpected problem (" + r.getLocalizedMessage()
+ ")";
System.err.println(msg);
- if (alignment != null)
- {
- break; // return what we got
- }
- else
- {
- throw new JalviewException(msg, r);
- }
+ r.printStackTrace();
+ break;
}
}
+ if (alignment == null)
+ {
+ return null;
+ }
+
/*
- * fetch and transfer genomic sequence features
+ * fetch and transfer genomic sequence features,
+ * fetch protein product and add as cross-reference
*/
for (String accId : allIds)
{
addFeaturesAndProduct(accId, alignment);
}
- inProgress = false;
+ for (SequenceI seq : alignment.getSequences())
+ {
+ getCrossReferences(seq);
+ }
+
return alignment;
}
@@ -165,34 +198,46 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
*/
protected void addFeaturesAndProduct(String accId, AlignmentI alignment)
{
+ if (alignment == null)
+ {
+ return;
+ }
+
try
{
/*
- * get 'dummy' genomic sequence with exon, cds and variation features
+ * get 'dummy' genomic sequence with gene, transcript,
+ * exon, cds and variation features
*/
- EnsemblOverlap gffFetcher = new EnsemblOverlap();
+ SequenceI genomicSequence = null;
+ EnsemblFeatures gffFetcher = new EnsemblFeatures(getDomain());
EnsemblFeatureType[] features = getFeaturesToFetch();
AlignmentI geneFeatures = gffFetcher.getSequenceRecords(accId,
features);
- if (geneFeatures.getHeight() > 0)
+ if (geneFeatures != null && geneFeatures.getHeight() > 0)
+ {
+ genomicSequence = geneFeatures.getSequenceAt(0);
+ }
+ if (genomicSequence != null)
{
/*
* transfer features to the query sequence
*/
- SequenceI genomicSequence = geneFeatures.getSequenceAt(0);
- SequenceI querySeq = alignment.findName(accId);
- transferFeatures(accId, genomicSequence, querySeq);
+ 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);
+ /*
+ * 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());
+ System.err.println(
+ "Error transferring Ensembl features: " + e.getMessage());
}
}
@@ -215,10 +260,11 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
String accId = querySeq.getName();
try
{
- AlignmentI protein = new EnsemblProtein().getSequenceRecords(accId);
+ AlignmentI protein = new EnsemblProtein(getDomain())
+ .getSequenceRecords(accId);
if (protein == null || protein.getHeight() == 0)
{
- System.out.println("Failed to retrieve protein for " + accId);
+ System.out.println("No protein product found for " + accId);
return;
}
SequenceI proteinSeq = protein.getSequenceAt(0);
@@ -229,13 +275,65 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
proteinSeq.createDatasetSequence();
querySeq.createDatasetSequence();
- MapList mapList = mapCdsToProtein(querySeq, proteinSeq);
+ MapList mapList = AlignmentUtils.mapCdsToProtein(querySeq,
+ proteinSeq);
if (mapList != null)
{
- Mapping map = new Mapping(proteinSeq.getDatasetSequence(), mapList);
- DBRefEntry dbr = new DBRefEntry(getDbSource(), getDbVersion(),
- accId, map);
+ // 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)
+ {
+ for (DBRefEntry up : uprots)
+ {
+ // locate local uniprot ref and map
+ List upx = DBRefUtils.searchRefs(upxrefs,
+ up.getAccessionId());
+ DBRefEntry upxref;
+ if (upx.size() != 0)
+ {
+ upxref = upx.get(0);
+
+ if (upx.size() > 1)
+ {
+ Cache.log.warn(
+ "Implementation issue - multiple uniprot acc on product sequence.");
+ }
+ }
+ 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);
+ }
+
+ }
+ }
+
+ /*
+ * 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)
{
@@ -246,55 +344,31 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
}
/**
- * Returns a mapping from dna to protein by inspecting sequence features of
- * type "CDS" on the dna.
+ * Get database xrefs from Ensembl, and attach them to the sequence
*
- * @param dnaSeq
- * @param proteinSeq
- * @return
+ * @param seq
*/
- protected MapList mapCdsToProtein(SequenceI dnaSeq, SequenceI proteinSeq)
+ protected void getCrossReferences(SequenceI seq)
{
- SequenceFeature[] sfs = dnaSeq.getSequenceFeatures();
- if (sfs == null)
+ while (seq.getDatasetSequence() != null)
{
- return null;
+ seq = seq.getDatasetSequence();
}
- List ranges = new ArrayList(50);
- SequenceOntology so = SequenceOntology.getInstance();
-
- int mappedDnaLength = 0;
-
- /*
- * Map CDS columns of dna to peptide. No need to worry about reverse strand
- * dna here since the retrieved sequence is as transcribed (reverse
- * complement for reverse strand), i.e in the same sense as the peptide.
- */
- for (SequenceFeature sf : sfs)
+ EnsemblXref xrefFetcher = new EnsemblXref(getDomain(), getDbSource(),
+ getEnsemblDataVersion());
+ List xrefs = xrefFetcher.getCrossReferences(seq.getName());
+ for (DBRefEntry xref : xrefs)
{
- /*
- * process a CDS feature (or a sub-type of CDS)
- */
- if (so.isA(sf.getType(), SequenceOntology.CDS))
- {
- ranges.add(new int[] { sf.getBegin(), sf.getEnd() });
- mappedDnaLength += Math.abs(sf.getEnd() - sf.getBegin()) + 1;
- }
+ seq.addDBRef(xref);
}
- int proteinLength = proteinSeq.getLength();
- List proteinRange = new ArrayList();
- proteinRange.add(new int[] { 1, proteinLength });
/*
- * dna length should map to protein (or protein minus stop codon)
+ * and add a reference to itself
*/
- if (mappedDnaLength == 3 * proteinLength
- || mappedDnaLength == 3 * (proteinLength + 1))
- {
- return new MapList(ranges, proteinRange, 3, 1);
- }
- return null;
+ DBRefEntry self = new DBRefEntry(getDbSource(), getEnsemblDataVersion(),
+ seq.getName());
+ seq.addDBRef(self);
}
/**
@@ -307,43 +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);
- FastaFile fr = new FastaFile(fp);
- if (fr.hasWarningMessage())
+ BufferedReader br = getSequenceReader(ids);
+ if (br == null)
{
- System.out.println(String.format(
- "Warning when retrieving %d ids %s\n%s", ids.size(),
- ids.toString(), fr.getWarningMessage()));
+ return alignment;
}
- else if (fr.getSeqs().size() != ids.size())
+
+ List 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", fr
- .getSeqs().size(), ids.size()));
+ "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())
+ 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")))
{
- DBRefUtils.parseToDbRef(sq, DBRefSource.ENSEMBL, "0", name);
+ // TODO JAL-3077 use true accession version in dbref
+ DBRefEntry dbref = DBRefUtils.parseToDbRef(seq, getDbSource(),
+ getEnsemblDataVersion(), name);
+ seq.addDBRef(dbref);
}
}
if (alignment == null)
@@ -359,6 +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
@@ -367,19 +493,43 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
@Override
protected URL getUrl(List ids) throws MalformedURLException
{
- // ids are not used - they go in the POST body instead
+ /*
+ * a single id is included in the URL path
+ * multiple ids go in the POST body instead
+ */
StringBuffer urlstring = new StringBuffer(128);
- urlstring.append(SEQUENCE_ID_URL);
-
+ 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=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
@@ -391,23 +541,11 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
}
@Override
- public boolean useGetRequest()
+ protected boolean useGetRequest()
{
return false;
}
- @Override
- public String getRequestMimeType()
- {
- return "application/json";
- }
-
- @Override
- public String getResponseMimeType()
- {
- return "text/x-fasta";
- }
-
/**
*
* @return the configured sequence return type for this source
@@ -434,112 +572,205 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
* backwards (for negative strand). Aborts and returns null if both positive
* and negative strand are found (this should not normally happen).
*
- * @param sfs
+ * @param sourceSequence
* @param accId
+ * @param start
+ * the start position of the sequence we are mapping to
* @return
*/
- protected MapList getGenomicRanges(SequenceFeature[] sfs, String accId)
+ protected MapList getGenomicRangesFromFeatures(SequenceI sourceSequence,
+ String accId, int start)
{
+ List sfs = getIdentifyingFeatures(sourceSequence,
+ accId);
+ if (sfs.isEmpty())
+ {
+ return null;
+ }
+
/*
- * generously size for initial number of cds regions
+ * 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();
-
- 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);
- }
+ 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, new RangeSorter(direction == 1));
-
- List to = new ArrayList();
- to.add(new int[] { 1, mappedLength });
-
+ Collections.sort(regions, direction == 1 ? IntRangeComparator.ASCENDING
+ : IntRangeComparator.DESCENDING);
+
+ List to = Arrays
+ .asList(new int[]
+ { start, start + mappedLength - 1 });
+
return new MapList(regions, to, 1, 1);
}
/**
- * Returns true if the sequence feature identifies positions of the genomic
- * sequence feature which are within the sequence being retrieved.
+ * 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 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, adjusting its start
- * and end range based on the 'overlap' ranges. Features which do not overlap
- * the target sequence are ignored, as are features with a parent other than
- * the target sequence id.
+ * 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 overlap
+ * @param mapping
+ * mapping from the sequence feature's coordinates to the target
+ * sequence
+ * @param forwardStrand
*/
protected void transferFeature(SequenceFeature sf,
- SequenceI targetSequence, MapList overlap)
+ SequenceI targetSequence, MapList mapping, boolean forwardStrand)
{
- String parent = (String) sf.getValue("Parent");
- if (parent != null && !parent.contains(targetSequence.getName()))
- {
- // this genomic feature belongs to a different transcript
- return;
- }
-
int start = sf.getBegin();
int end = sf.getEnd();
- int[] mappedRange = overlap.locateInTo(start, end);
-
+ int[] mappedRange = mapping.locateInTo(start, end);
+
if (mappedRange != null)
{
- SequenceFeature copy = new SequenceFeature(sf);
- int offset = targetSequence.getStart() - 1;
- copy.setBegin(offset + Math.min(mappedRange[0], mappedRange[1]));
- copy.setEnd(offset + Math.max(mappedRange[0], mappedRange[1]));
+ 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)));
+ }
}
-
}
/**
@@ -548,51 +779,154 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
* @param accessionId
* @param sourceSequence
* @param targetSequence
+ * @return true if any features were transferred, else false
*/
- protected void transferFeatures(String accessionId,
+ protected boolean transferFeatures(String accessionId,
SequenceI sourceSequence, SequenceI targetSequence)
{
if (sourceSequence == null || targetSequence == null)
{
- return;
+ return false;
}
- SequenceFeature[] sfs = sourceSequence.getSequenceFeatures();
- MapList overlap = getGenomicRanges(sfs, accessionId);
+// long start = System.currentTimeMillis();
+ List 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;
+ }
- final boolean forwardStrand = overlap.isFromForwardStrand();
+ /**
+ * 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 sfs,
+ SequenceI targetSequence, MapList mapping, String parentId)
+ {
+ final boolean forwardStrand = mapping.isFromForwardStrand();
/*
- * sort features by start position (descending if reverse strand)
- * before transferring (in forwards order) to the target sequence
+ * 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
*/
- Arrays.sort(sfs, new Comparator()
+ SequenceFeatures.sortFeatures(sfs, forwardStrand);
+
+ boolean transferred = false;
+ for (SequenceFeature sf : sfs)
{
- @Override
- public int compare(SequenceFeature o1, SequenceFeature o2)
+ if (retainFeature(sf, parentId))
{
- int c = Integer.compare(o1.getBegin(), o2.getBegin());
- return forwardStrand ? c : -c;
+ 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);
+ // using contains to allow for prefix "gene:", "transcript:" etc
+ if (parent != null
+ && !parent.toUpperCase().contains(identifier.toUpperCase()))
+ {
+ // this genomic feature belongs to a different transcript
+ return false;
+ }
+ return true;
+ }
+
+ @Override
+ 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 findFeatures(SequenceI sequence,
+ String term, String parentId)
+ {
+ List result = new ArrayList<>();
+
+ List sfs = sequence.getFeatures()
+ .getFeaturesByOntology(term);
for (SequenceFeature sf : sfs)
{
- if (retainFeature(sf.getType()))
+ String parent = (String) sf.getValue(PARENT);
+ if (parent != null && parent.equalsIgnoreCase(parentId))
{
- transferFeature(sf, targetSequence, overlap);
+ result.add(sf);
}
}
+
+ return result;
}
/**
- * Answers true if the feature type is one to attach to the retrieved sequence
+ * 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
+ * needed because NMD_transcript_variant behaves like 'transcript' in Ensembl
+ * although strictly speaking it is not (it is a sub-type of
+ * sequence_variant).
*
- * @param type
+ * @param featureType
* @return
*/
- protected boolean retainFeature(@SuppressWarnings("unused") String type)
+ public static boolean isTranscript(String featureType)
{
- return true; // default is to keep all
+ return SequenceOntologyI.NMD_TRANSCRIPT_VARIANT.equals(featureType)
+ || SequenceOntologyFactory.getInstance().isA(featureType,
+ SequenceOntologyI.TRANSCRIPT);
}
}