import jalview.io.gff.SequenceOntologyFactory;
import jalview.io.gff.SequenceOntologyI;
import jalview.util.MapList;
+import jalview.util.StringUtils;
-import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
{
private static final String GENE_PREFIX = "gene:";
- // TODO modify to accept other species e.g. ENSMUSGnnn
- private static final Regex ACCESSION_REGEX = new Regex(
- "(ENSG|ENST)[0-9]{11}$");
+ /*
+ * accepts anything as we will attempt lookup of gene or
+ * transcript id or gene name
+ */
+ private static final Regex ACCESSION_REGEX = new Regex(".*");
private static final EnsemblFeatureType[] FEATURES_TO_FETCH = {
EnsemblFeatureType.gene, EnsemblFeatureType.transcript,
}
/**
- * Builds an alignment of all transcripts for the requested gene:
+ * Returns an alignment containing the gene(s) for the given gene or
+ * transcript identifier, or external identifier (e.g. Uniprot id). If given a
+ * gene name or external identifier, returns any related gene sequences found
+ * for model organisms. If only a single gene is queried for, then its
+ * transcripts are also retrieved and added to the alignment. <br>
+ * Method:
* <ul>
+ * <li>resolves a transcript identifier by looking up its parent gene id</li>
+ * <li>resolves an external identifier by looking up xref-ed gene ids</li>
* <li>fetches the gene sequence</li>
* <li>fetches features on the sequence</li>
* <li>identifies "transcript" features whose Parent is the requested gene</li>
* <li>aligns each transcript against the gene sequence based on the position
* mappings</li>
* </ul>
+ *
+ * @param query
+ * one or more identifiers separated by a space
+ * @return an alignment containing one or more genes, and possibly
+ * transcripts, or null
*/
@Override
public AlignmentI getSequenceRecords(String query) throws Exception
{
- List<String> transcriptsWanted = null;
+ // todo: tidy up handling of one or multiple accession ids
+ String[] queries = query.split(getAccessionSeparator());
+ /*
+ * if given a transcript id, look up its gene parent
+ */
if (isTranscriptIdentifier(query))
{
- transcriptsWanted = Arrays.asList(query
- .split(getAccessionSeparator()));
- query = getGeneForTranscript(query);
+ // we are assuming all transcripts have the same gene parent here
+ query = new EnsemblLookup().getParent(queries[0]);
if (query == null)
{
return null;
}
}
+ /*
+ * if given a gene or other external name, lookup and fetch
+ * the corresponding gene for all model organisms
+ */
+ if (!isGeneIdentifier(query))
+ {
+ List<String> geneIds = new EnsemblSymbol().getIds(query);
+ if (geneIds.isEmpty())
+ {
+ return null;
+ }
+ String theIds = StringUtils.listToDelimitedString(geneIds,
+ getAccessionSeparator());
+ return getSequenceRecords(theIds);
+ }
+
AlignmentI al = super.getSequenceRecords(query);
- if (al.getHeight() > 0)
+
+ /*
+ * if we retrieved a single gene, get its transcripts as well
+ */
+ if (al.getHeight() == 1)
{
- getTranscripts(al, query, transcriptsWanted);
+ getTranscripts(al, query);
}
return al;
}
/**
- * Gets the parent gene identifier for a given transcript identifier, by
- * retrieving 'transcript' features overlapping the transcript, and finding
- * the Parent property of the feature whose id is the given identifier.
+ * Attempts to get Ensembl stable identifiers for model organisms for a gene
+ * name by calling the xrefs symbol REST service to resolve the gene name.
*
* @param query
* @return
*/
- protected String getGeneForTranscript(String transcriptId)
+ protected String getGeneIdentifiersForName(String query)
{
- String geneId = null;
-
- /*
- * reduce multiple transcripts (e.g. from Uniprot x-ref) to the first
- * one only as representative (they should all have the same gene)
- */
- transcriptId = transcriptId.split(getAccessionSeparator())[0];
-
- try
+ List<String> ids = new EnsemblSymbol().getIds(query);
+ if (ids != null)
{
- EnsemblFeatureType[] geneFeature = new EnsemblFeatureType[] { EnsemblFeatureType.transcript };
- AlignmentI al = new EnsemblFeatures().getSequenceRecords(
- transcriptId, geneFeature);
- if (al != null && al.getHeight() > 0)
+ for (String id : ids)
{
- SequenceFeature[] sfs = al.getSequenceAt(0).getSequenceFeatures();
- if (sfs != null)
+ if (isGeneIdentifier(id))
{
- for (SequenceFeature sf : sfs)
- {
- if (transcriptId.equals(getTranscriptId(sf)))
- {
- String parent = (String) sf.getValue(PARENT);
- if (parent != null && parent.startsWith(GENE_PREFIX))
- {
- geneId = parent.substring(5);
- }
- break;
- }
- }
+ return id;
}
}
- return geneId;
- } catch (IOException e)
- {
- System.err.println("Error retrieving gene id for " + transcriptId
- + ": " + e.getMessage());
- return null;
}
+ return null;
}
/**
*
* @param al
* @param accId
- * @param transcriptsWanted
- * optional list of transcript ids to filter by
* @throws Exception
*/
- protected void getTranscripts(AlignmentI al, String accId,
- List<String> transcriptsWanted)
+ protected void getTranscripts(AlignmentI al, String accId)
throws Exception
{
SequenceI gene = al.getSequenceAt(0);
List<SequenceFeature> transcriptFeatures = getTranscriptFeatures(accId,
- gene, transcriptsWanted);
+ gene);
for (SequenceFeature transcriptFeature : transcriptFeatures)
{
transcript.getDatasetSequence(), mapping, parentId);
/*
+ * fetch and save cross-references
+ */
+ super.getCrossReferences(transcript);
+
+ /*
* and finally fetch the protein product and save as a cross-reference
*/
new EnsemblCdna().addProteinProduct(transcript);
*
* @param accId
* @param geneSequence
- * @param transcriptsWanted
- * optional list of ids to filter on
* @return
*/
protected List<SequenceFeature> getTranscriptFeatures(String accId,
- SequenceI geneSequence, List<String> transcriptsWanted)
+ SequenceI geneSequence)
{
List<SequenceFeature> transcriptFeatures = new ArrayList<SequenceFeature>();
{
if (isTranscript(sf.getType()))
{
- if (transcriptsWanted != null)
- {
- String transcriptId = (String) sf.getValue("transcript_id");
- if (!transcriptsWanted.contains(transcriptId))
- {
- // continue;
- }
- }
String parent = (String) sf.getValue(PARENT);
if (parentIdentifier.equals(parent))
{
--- /dev/null
+package jalview.ext.ensembl;
+
+import jalview.datamodel.AlignmentI;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.Arrays;
+import java.util.List;
+
+import org.json.simple.JSONObject;
+import org.json.simple.parser.JSONParser;
+import org.json.simple.parser.ParseException;
+
+public class EnsemblLookup extends EnsemblRestClient
+{
+
+ @Override
+ public String getDbName()
+ {
+ return "ENSEMBL";
+ }
+
+ @Override
+ public AlignmentI getSequenceRecords(String queries) throws Exception
+ {
+ return null;
+ }
+
+ @Override
+ protected URL getUrl(List<String> ids) throws MalformedURLException
+ {
+ String identifier = ids.get(0);
+ return getUrl(identifier);
+ }
+
+ /**
+ * @param identifier
+ * @return
+ */
+ protected URL getUrl(String identifier)
+ {
+ String url = ENSEMBL_REST + "/lookup/id/" + identifier
+ + "?content-type=application/json";
+ try
+ {
+ return new URL(url);
+ } catch (MalformedURLException e)
+ {
+ return null;
+ }
+ }
+
+ @Override
+ protected boolean useGetRequest()
+ {
+ return true;
+ }
+
+ @Override
+ protected String getRequestMimeType(boolean multipleIds)
+ {
+ return "application/json";
+ }
+
+ @Override
+ protected String getResponseMimeType()
+ {
+ return "application/json";
+ }
+
+ /**
+ * Calls the Ensembl lookup REST endpoint and retrieves the 'Parent' for the
+ * given identifier, or null if not found
+ *
+ * @param identifier
+ * @return
+ */
+ public String getParent(String identifier)
+ {
+ List<String> ids = Arrays.asList(new String[] { identifier });
+
+ BufferedReader br = null;
+ try
+ {
+ URL url = getUrl(identifier);
+ if (url != null)
+ {
+ br = getHttpResponse(url, ids);
+ }
+ return (parseResponse(br));
+ } catch (IOException e)
+ {
+ // ignore
+ return null;
+ } finally
+ {
+ if (br != null)
+ {
+ try
+ {
+ br.close();
+ } catch (IOException e)
+ {
+ // ignore
+ }
+ }
+ }
+ }
+
+ /**
+ * Parses "Parent" from the JSON response and returns the value, or null if
+ * not found
+ *
+ * @param br
+ * @return
+ * @throws IOException
+ */
+ protected String parseResponse(BufferedReader br) throws IOException
+ {
+ String parent = null;
+ JSONParser jp = new JSONParser();
+ try
+ {
+ JSONObject val = (JSONObject) jp.parse(br);
+ parent = val.get("Parent").toString();
+ } catch (ParseException e)
+ {
+ // ignore
+ }
+ return parent;
+ }
+
+}
--- /dev/null
+package jalview.ext.ensembl;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+
+import org.json.simple.JSONArray;
+import org.json.simple.JSONObject;
+import org.json.simple.parser.JSONParser;
+import org.json.simple.parser.ParseException;
+
+public class EnsemblSymbol extends EnsemblXref
+{
+ /**
+ * Returns the first "id" value in gene identifier format from the JSON
+ * response, or null if none found
+ *
+ * @param br
+ * @return
+ * @throws IOException
+ */
+ protected String parseResponse(BufferedReader br)
+ throws IOException
+ {
+ JSONParser jp = new JSONParser();
+ String result = null;
+ try
+ {
+ JSONArray responses = (JSONArray) jp.parse(br);
+ Iterator rvals = responses.iterator();
+ while (rvals.hasNext())
+ {
+ JSONObject val = (JSONObject) rvals.next();
+ String id = val.get("id").toString();
+ if (id != null && isGeneIdentifier(id))
+ {
+ result = id;
+ break;
+ }
+ }
+ } catch (ParseException e)
+ {
+ // ignore
+ }
+ return result;
+ }
+
+ protected URL getUrl(String id, Species species)
+ {
+ String url = ENSEMBL_REST + "/xrefs/symbol/" + species.toString() + "/"
+ + id
+ + "?content-type=application/json";
+ try
+ {
+ return new URL(url);
+ } catch (MalformedURLException e)
+ {
+ return null;
+ }
+ }
+
+ /**
+ * Calls the Ensembl xrefs REST 'symbol' endpoint and retrieves any gene ids
+ * for the given identifier, for any known model organisms
+ *
+ * @param identifier
+ * @return
+ */
+ public List<String> getIds(String identifier)
+ {
+ List<String> result = new ArrayList<String>();
+ List<String> ids = new ArrayList<String>();
+ ids.add(identifier);
+
+ String[] queries = identifier.split(getAccessionSeparator());
+ BufferedReader br = null;
+ try
+ {
+ for (String query : queries)
+ {
+ for (Species taxon : Species.values())
+ {
+ if (taxon.isModelOrganism())
+ {
+ URL url = getUrl(query, taxon);
+ if (url != null)
+ {
+ br = getHttpResponse(url, ids);
+ }
+ String geneId = parseResponse(br);
+ if (geneId != null)
+ {
+ result.add(geneId);
+ }
+ }
+ }
+ }
+ } catch (IOException e)
+ {
+ // ignore
+ } finally
+ {
+ if (br != null)
+ {
+ try
+ {
+ br.close();
+ } catch (IOException e)
+ {
+ // ignore
+ }
+ }
+ }
+ return result;
+ }
+
+}
--- /dev/null
+package jalview.ext.ensembl;
+
+/**
+ * Selected species identifiers used by Ensembl
+ *
+ * @author gmcarstairs
+ * @see http://rest.ensembl.org/info/species?content-type=text/xml
+ */
+enum Species
+{
+ /*
+ * using any suitably readable alias as the enum name; these are all
+ * valid species parameters to Ensembl REST services where applicable
+ */
+ human(true), mouse(true), s_cerevisiae(true), cow(false), pig(false),
+ rat(true), celegans(true), sheep(false), horse(false), gorilla(false),
+ rabbit(false), gibbon(false), dog(false), orangutan(false),
+ xenopus(true), chimpanzee(false), cat(false), zebrafish(true), chicken(
+ true), dmelanogaster(true);
+
+ boolean modelOrganism;
+
+ private Species(boolean model)
+ {
+ this.modelOrganism = model;
+ }
+
+ boolean isModelOrganism()
+ {
+ return modelOrganism;
+ }
+}
import jalview.io.gff.SequenceOntologyLite;
import jalview.util.MapList;
-import java.util.Arrays;
import java.util.List;
import org.testng.annotations.AfterClass;
* with no filter
*/
List<SequenceFeature> features = testee.getTranscriptFeatures(geneId,
- genomic, null);
+ genomic);
assertEquals(3, features.size());
assertSame(sf1, features.get(0));
assertSame(sf2, features.get(1));
assertSame(sf3, features.get(2));
-
- /*
- * with filter
- */
- List<String> ids = Arrays.asList(new String[] { "transcript2",
- "transcript3" });
- features = testee.getTranscriptFeatures(geneId, genomic, ids);
- assertEquals(2, features.size());
- assertSame(sf2, features.get(0));
- assertSame(sf3, features.get(1));
}
/**
git://source.jalview.org / jalview.git / commitdiff