X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblSeqProxy.java;h=b2ebb1ac5dc4db1c833c16def46b67431cc3de16;hb=aad3640b07f836362df7ea025fa09127a0a06145;hp=b4c708d8826f2a96e2ec5781a562405b508227d3;hpb=a57f7818a994eaabd11db26e83bc23832cc7b359;p=jalview.git
diff --git a/src/jalview/ext/ensembl/EnsemblSeqProxy.java b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
index b4c708d..b2ebb1a 100644
--- a/src/jalview/ext/ensembl/EnsemblSeqProxy.java
+++ b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
@@ -1,7 +1,28 @@
+/*
+ * 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;
@@ -9,12 +30,15 @@ import jalview.datamodel.DBRefSource;
import jalview.datamodel.Mapping;
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.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.IOException;
@@ -23,7 +47,6 @@ import java.net.URL;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
-import java.util.Comparator;
import java.util.List;
/**
@@ -36,16 +59,6 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
{
private static final String ALLELES = "alleles";
- private static final List CROSS_REFERENCES = Arrays
- .asList(new String[] { "CCDS", "Uniprot/SWISSPROT",
- "Uniprot/SPTREMBL" });
-
- protected static final String CONSEQUENCE_TYPE = "consequence_type";
-
- protected static final String PARENT = "Parent";
-
- protected static final String ID = "ID";
-
protected static final String NAME = "Name";
protected static final String DESCRIPTION = "description";
@@ -61,7 +74,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
GENOMIC("genomic"),
/**
- * type=cdna to fetch dna including UTRs
+ * type=cdna to fetch coding dna including UTRs
*/
CDNA("cdna"),
@@ -94,26 +107,6 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
}
/**
- * A comparator to sort ranges into ascending start position order
- */
- private class RangeSorter implements Comparator
- {
- 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]);
- }
-
- }
-
- /**
* Default constructor (to use rest.ensembl.org)
*/
public EnsemblSeqProxy()
@@ -140,8 +133,8 @@ 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;
@@ -164,6 +157,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
+ " chunks. Unexpected problem (" + r.getLocalizedMessage()
+ ")";
System.err.println(msg);
+ r.printStackTrace();
break;
}
}
@@ -209,14 +203,15 @@ 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());
EnsemblFeatureType[] features = getFeaturesToFetch();
AlignmentI geneFeatures = gffFetcher.getSequenceRecords(accId,
features);
- if (geneFeatures.getHeight() > 0)
+ if (geneFeatures != null && geneFeatures.getHeight() > 0)
{
genomicSequence = geneFeatures.getSequenceAt(0);
}
@@ -225,7 +220,7 @@ 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))
{
@@ -238,8 +233,8 @@ 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());
}
}
@@ -277,22 +272,65 @@ 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
SequenceI ds = proteinSeq.getDatasetSequence();
- ds.setSourceDBRef(proteinSeq.getSourceDBRef());
+ // TODO: Verify ensp primary ref is on proteinSeq.getDatasetSequence()
Mapping map = new Mapping(ds, mapList);
- DBRefEntry dbr = new DBRefEntry(getDbSource(), getDbVersion(),
- accId, map);
+ 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);
+ AlignmentUtils.computeProteinFeatures(querySeq, proteinSeq,
+ mapList);
}
} catch (Exception e)
{
@@ -314,32 +352,20 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
seq = seq.getDatasetSequence();
}
- EnsemblXref xrefFetcher = new EnsemblXref(getDomain());
- List xrefs = xrefFetcher.getCrossReferences(seq.getName(),
- getCrossReferenceDatabases());
+ EnsemblXref xrefFetcher = new EnsemblXref(getDomain(), getDbSource(),
+ getEnsemblDataVersion());
+ List xrefs = xrefFetcher.getCrossReferences(seq.getName());
for (DBRefEntry xref : xrefs)
{
seq.addDBRef(xref);
- /*
- * Save any Uniprot xref to be the reference for SIFTS mapping
- */
- if (DBRefSource.UNIPROT.equals(xref.getSource()))
- {
- seq.setSourceDBRef(xref);
- }
}
- }
- /**
- * Returns a list of database names to be used when fetching cross-references.
- * Specifically, the names are used to filter data returned by the Ensembl
- * xrefs REST service on the value in field 'dbname'.
- *
- * @return
- */
- protected List getCrossReferenceDatabases()
- {
- return CROSS_REFERENCES;
+ /*
+ * and add a reference to itself
+ */
+ DBRefEntry self = new DBRefEntry(getDbSource(), getEnsemblDataVersion(),
+ seq.getName());
+ seq.addDBRef(self);
}
/**
@@ -352,8 +378,8 @@ 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())
{
@@ -361,18 +387,23 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
throw new JalviewException("ENSEMBL Rest API not available.");
}
FileParse fp = getSequenceReader(ids);
+ if (fp == 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()));
+ 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())
{
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",
+ fr.getSeqs().size(), ids.size()));
}
if (fr.getSeqs().size() == 1 && fr.getSeqs().get(0).getLength() == 0)
@@ -385,9 +416,8 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
if (fr.getSeqs().size() > 0)
{
- AlignmentI seqal = new Alignment(
- fr.getSeqsAsArray());
- for (SequenceI sq:seqal.getSequences())
+ AlignmentI seqal = new Alignment(fr.getSeqsAsArray());
+ for (SequenceI sq : seqal.getSequences())
{
if (sq.getDescription() == null)
{
@@ -397,7 +427,9 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
if (ids.contains(name)
|| ids.contains(name.replace("ENSP", "ENST")))
{
- DBRefUtils.parseToDbRef(sq, DBRefSource.ENSEMBL, "0", name);
+ DBRefEntry dbref = DBRefUtils.parseToDbRef(sq, getDbSource(),
+ getEnsemblDataVersion(), name);
+ sq.addDBRef(dbref);
}
}
if (alignment == null)
@@ -435,11 +467,28 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
urlstring.append("?type=").append(getSourceEnsemblType().getType());
urlstring.append(("&Accept=text/x-fasta"));
+ 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
@@ -503,8 +552,9 @@ 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;
}
@@ -513,11 +563,11 @@ 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)
{
/*
@@ -532,22 +582,22 @@ 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);
- 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
- {
+ 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);
@@ -562,7 +612,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
}
}
}
-
+
if (regions.isEmpty())
{
System.out.println("Failed to identify target sequence for " + accId
@@ -574,11 +624,13 @@ 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 RangeSorter(direction == 1));
-
- List to = Arrays.asList(new int[] { start,
- start + mappedLength - 1 });
-
+ 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);
}
@@ -622,21 +674,26 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
int start = sf.getBegin();
int end = sf.getEnd();
int[] mappedRange = mapping.locateInTo(start, end);
-
+
if (mappedRange != null)
{
- SequenceFeature copy = new SequenceFeature(sf);
- copy.setBegin(Math.min(mappedRange[0], mappedRange[1]));
- copy.setEnd(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))
+ if (!forwardStrand && SequenceOntologyFactory.getInstance()
+ .isA(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT))
{
reverseComplementAlleles(copy);
}
@@ -691,16 +748,21 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
{
complement.append(",");
}
- if ("HGMD_MUTATION".equalsIgnoreCase(allele))
+
+ /*
+ * 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
{
- char[] alleles = allele.toCharArray();
- for (int i = alleles.length - 1; i >= 0; i--)
+ for (int i = allele.length() - 1; i >= 0; i--)
{
- complement.append(Dna.getComplement(alleles[i]));
+ complement.append(Dna.getComplement(allele.charAt(i)));
}
}
}
@@ -721,10 +783,11 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
return false;
}
- // long start = System.currentTimeMillis();
- SequenceFeature[] sfs = sourceSequence.getSequenceFeatures();
- MapList mapping = getGenomicRangesFromFeatures(sourceSequence, accessionId,
- targetSequence.getStart());
+// long start = System.currentTimeMillis();
+ List sfs = sourceSequence.getFeatures()
+ .getPositionalFeatures();
+ MapList mapping = getGenomicRangesFromFeatures(sourceSequence,
+ accessionId, targetSequence.getStart());
if (mapping == null)
{
return false;
@@ -732,10 +795,10 @@ 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;
}
@@ -744,13 +807,13 @@ 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();
@@ -760,10 +823,10 @@ 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))
{
@@ -775,33 +838,6 @@ 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
@@ -826,7 +862,8 @@ 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;
@@ -843,33 +880,30 @@ 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();
-
- SequenceFeature[] sfs = sequence.getSequenceFeatures();
- if (sfs != null) {
- SequenceOntologyI so = SequenceOntologyFactory.getInstance();
- for (SequenceFeature sf :sfs) {
- if (so.isA(sf.getType(), type))
- {
- String parent = (String) sf.getValue(PARENT);
- if (parent.equals(parentId))
- {
- result.add(sf);
- }
- }
+ List result = new ArrayList<>();
+
+ List 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;
}