*/
package jalview.ext.ensembl;
+import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.GeneLociI;
+import jalview.util.MapList;
import java.io.BufferedReader;
import java.io.IOException;
import java.net.MalformedURLException;
import java.net.URL;
import java.util.Arrays;
+import java.util.Collections;
import java.util.List;
+import java.util.function.Function;
import org.json.simple.JSONObject;
import org.json.simple.parser.JSONParser;
import org.json.simple.parser.ParseException;
/**
- * A client for the Ensembl lookup REST endpoint, used to find the gene
- * identifier given a gene, transcript or protein identifier.
+ * A client for the Ensembl /lookup REST endpoint, used to find the gene
+ * identifier given a gene, transcript or protein identifier, or to extract the
+ * species or chromosomal coordinates from the same service response
*
* @author gmcarstairs
*/
public class EnsemblLookup extends EnsemblRestClient
{
+ private static final String SPECIES = "species";
+
/**
* Default constructor (to use rest.ensembl.org)
*/
}
/**
- * Returns the gene id related to the given identifier, which may be for a
- * gene, transcript or protein
+ * Returns the gene id related to the given identifier (which may be for a
+ * gene, transcript or protein)
*
* @param identifier
* @return
*/
public String getGeneId(String identifier)
{
- return getGeneId(identifier, null);
+ return (String) getResult(identifier, null, br -> parseGeneId(br));
}
/**
- * Calls the Ensembl lookup REST endpoint and retrieves the 'Parent' for the
+ * Calls the Ensembl lookup REST endpoint and retrieves the 'species' for the
* given identifier, or null if not found
*
* @param identifier
+ * @return
+ */
+ public String getSpecies(String identifier)
+ {
+ return (String) getResult(identifier, null,
+ br -> getAttribute(br, SPECIES));
+ }
+
+ /**
+ * Calls the /lookup/id rest service and delegates parsing of the JSON
+ * response to the supplied parser
+ *
+ * @param identifier
* @param objectType
* (optional)
+ * @param parser
* @return
*/
- public String getGeneId(String identifier, String objectType)
+ protected Object getResult(String identifier, String objectType,
+ Function<BufferedReader, Object> parser)
{
List<String> ids = Arrays.asList(new String[] { identifier });
{
br = getHttpResponse(url, ids);
}
- return br == null ? null : parseResponse(br);
+ return br == null ? null : parser.apply(br);
} catch (IOException e)
{
// ignore
}
/**
+ * Answers the value of 'attribute' from the JSON response, or null if not
+ * found
+ *
+ * @param br
+ * @param attribute
+ * @return
+ */
+ protected String getAttribute(BufferedReader br, String attribute)
+ {
+ String value = null;
+ JSONParser jp = new JSONParser();
+ try
+ {
+ JSONObject val = (JSONObject) jp.parse(br);
+ value = val.get(attribute).toString();
+ } catch (ParseException | NullPointerException | IOException e)
+ {
+ // ignore
+ }
+ return value;
+ }
+
+ /**
* Parses the JSON response and returns the gene identifier, or null if not
* found. If the returned object_type is Gene, returns the id, if Transcript
* returns the Parent. If it is Translation (peptide identifier), then the
- * Parent is the transcript identifier, so we redo the search with this value.
+ * Parent is the transcript identifier, so we redo the search with this value,
+ * specifying that object_type should be Transcript.
*
* @param br
* @return
- * @throws IOException
*/
- protected String parseResponse(BufferedReader br) throws IOException
+ protected String parseGeneId(BufferedReader br)
{
String geneId = null;
JSONParser jp = new JSONParser();
if (OBJECT_TYPE_GENE.equalsIgnoreCase(type))
{
// got the gene - just returns its id
- geneId = val.get(ID).toString();
+ geneId = val.get(JSON_ID).toString();
}
else if (OBJECT_TYPE_TRANSCRIPT.equalsIgnoreCase(type))
{
{
// got the protein - get its Parent, restricted to type Transcript
String transcriptId = val.get(PARENT).toString();
- geneId = getGeneId(transcriptId, OBJECT_TYPE_TRANSCRIPT);
+ geneId = (String) getResult(transcriptId, OBJECT_TYPE_TRANSCRIPT,
+ reader -> parseGeneId(reader));
}
- } catch (ParseException e)
+ } catch (ParseException | IOException e)
{
// ignore
}
return geneId;
}
+ /**
+ * Calls the /lookup/id rest service for the given id, and if successful,
+ * parses and returns the gene's chromosomal coordinates
+ *
+ * @param geneId
+ * @return
+ */
+ public GeneLociI getGeneLoci(String geneId)
+ {
+ return (GeneLociI) getResult(geneId, OBJECT_TYPE_GENE,
+ br -> parseGeneLoci(br));
+ }
+
+ /**
+ * Parses the /lookup/id response for species, asssembly_name,
+ * seq_region_name, start, end and returns an object that wraps them, or null
+ * if unsuccessful
+ *
+ * @param br
+ * @return
+ */
+ GeneLociI parseGeneLoci(BufferedReader br)
+ {
+ JSONParser jp = new JSONParser();
+ try
+ {
+ JSONObject val = (JSONObject) jp.parse(br);
+ final String species = val.get("species").toString();
+ final String assembly = val.get("assembly_name").toString();
+ final String chromosome = val.get("seq_region_name").toString();
+ String strand = val.get("strand").toString();
+ int start = Integer.parseInt(val.get("start").toString());
+ int end = Integer.parseInt(val.get("end").toString());
+ int fromEnd = end - start + 1;
+ boolean reverseStrand = "-1".equals(strand);
+ int toStart = reverseStrand ? end : start;
+ int toEnd = reverseStrand ? start : end;
+ List<int[]> fromRange = Collections.singletonList(new int[] { 1,
+ fromEnd });
+ List<int[]> toRange = Collections.singletonList(new int[] { toStart,
+ toEnd });
+ final MapList map = new MapList(fromRange, toRange, 1, 1);
+ return new GeneLociI()
+ {
+
+ @Override
+ public String getSpeciesId()
+ {
+ return species == null ? "" : species;
+ }
+
+ @Override
+ public String getAssemblyId()
+ {
+ return assembly;
+ }
+
+ @Override
+ public String getChromosomeId()
+ {
+ return chromosome;
+ }
+
+ @Override
+ public MapList getMap()
+ {
+ return map;
+ }
+ };
+ } catch (ParseException | NullPointerException | IOException
+ | NumberFormatException | ClassCastException e)
+ {
+ Cache.log.error("Error looking up gene loci: " + e.getMessage());
+ e.printStackTrace();
+ }
+ return null;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff