import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefSource;
+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.ArrayList;
+import java.util.Collections;
import java.util.Iterator;
import java.util.List;
private static final String MAPPINGS = "mappings";
+ private static final String CDS = "cds";
+
+ private static final String CDNA = "cdna";
+
/**
* Default constructor (to use rest.ensembl.org)
*/
}
/**
+ * Calls the REST /map/cds/id service, and returns a DBRefEntry holding the
+ * returned chromosomal coordinates, or returns null if the call fails
+ *
+ * @param division
+ * e.g. Ensembl, EnsemblMetazoa
+ * @param accession
+ * e.g. ENST00000592782, Y55B1AR.1.1
+ * @param start
+ * @param end
+ * @return
+ */
+ public GeneLociI getCdsMapping(String division, String accession,
+ int start, int end)
+ {
+ return getIdMapping(division, accession, start, end, CDS);
+ }
+
+ /**
+ * Calls the REST /map/cdna/id service, and returns a DBRefEntry holding the
+ * returned chromosomal coordinates, or returns null if the call fails
+ *
+ * @param division
+ * e.g. Ensembl, EnsemblMetazoa
+ * @param accession
+ * e.g. ENST00000592782, Y55B1AR.1.1
+ * @param start
+ * @param end
+ * @return
+ */
+ public GeneLociI getCdnaMapping(String division, String accession,
+ int start, int end)
+ {
+ return getIdMapping(division, accession, start, end, CDNA);
+ }
+
+ GeneLociI getIdMapping(String division, String accession, int start,
+ int end, String cdsOrCdna)
+ {
+ URL url = null;
+ BufferedReader br = null;
+
+ try
+ {
+ String domain = new EnsemblInfo().getDomain(division);
+ if (domain != null)
+ {
+ url = getIdMapUrl(domain, accession, start, end, cdsOrCdna);
+ br = getHttpResponse(url, null);
+ if (br != null)
+ {
+ return (parseIdMappingResponse(br, accession, domain));
+ }
+ }
+ return null;
+ } catch (Throwable t)
+ {
+ System.out.println("Error calling " + url + ": " + t.getMessage());
+ return null;
+ } finally
+ {
+ if (br != null)
+ {
+ try
+ {
+ br.close();
+ } catch (IOException e)
+ {
+ // ignore
+ }
+ }
+ }
+ }
+
+ /**
* Constructs a URL to the /map/cds/<id> or /map/cdna/<id> REST service. The
* REST call is to either ensembl or ensemblgenomes, as determined from the
* division, e.g. Ensembl or EnsemblProtists.
return new URL(url);
}
+ /**
+ * Parses the JSON response from the /map/cds/ or /map/cdna REST service. The
+ * format is
+ *
+ * <pre>
+ * {"mappings":
+ * [
+ * {"assembly_name":"TAIR10","end":2501311,"seq_region_name":"1","gap":0,
+ * "strand":-1,"coord_system":"chromosome","rank":0,"start":2501114},
+ * {"assembly_name":"TAIR10","end":2500815,"seq_region_name":"1","gap":0,
+ * "strand":-1,"coord_system":"chromosome","rank":0,"start":2500714}
+ * ]
+ * }
+ * </pre>
+ *
+ * @param br
+ * @param accession
+ * @param domain
+ * @return
+ */
+ GeneLociI parseIdMappingResponse(BufferedReader br, String accession,
+ String domain)
+ {
+ JSONParser jp = new JSONParser();
+
+ try
+ {
+ JSONObject parsed = (JSONObject) jp.parse(br);
+ JSONArray mappings = (JSONArray) parsed.get(MAPPINGS);
+
+ Iterator rvals = mappings.iterator();
+ String assembly = null;
+ String chromosome = null;
+ int fromEnd = 0;
+ List<int[]> regions = new ArrayList<>();
+
+ while (rvals.hasNext())
+ {
+ JSONObject val = (JSONObject) rvals.next();
+ JSONObject original = (JSONObject) val.get("original");
+ fromEnd = Integer.parseInt(original.get("end").toString());
+
+ JSONObject mapped = (JSONObject) val.get(MAPPED);
+ int start = Integer.parseInt(mapped.get("start").toString());
+ int end = Integer.parseInt(mapped.get("end").toString());
+ String ass = mapped.get("assembly_name").toString();
+ if (assembly != null && !assembly.equals(ass))
+ {
+ System.err
+ .println("EnsemblMap found multiple assemblies - can't resolve");
+ return null;
+ }
+ assembly = ass;
+ String chr = mapped.get("seq_region_name").toString();
+ if (chromosome != null && !chromosome.equals(chr))
+ {
+ System.err
+ .println("EnsemblMap found multiple chromosomes - can't resolve");
+ return null;
+ }
+ chromosome = chr;
+ String strand = mapped.get("strand").toString();
+ if ("-1".equals(strand))
+ {
+ regions.add(new int[] { end, start });
+ }
+ else
+ {
+ regions.add(new int[] { start, end });
+ }
+ }
+
+ /*
+ * processed all mapped regions on chromosome, assemble the result,
+ * having first fetched the species id for the accession
+ */
+ final String species = new EnsemblLookup(domain)
+ .getSpecies(accession);
+ final String as = assembly;
+ final String chr = chromosome;
+ List<int[]> fromRange = Collections.singletonList(new int[] { 1,
+ fromEnd });
+ final MapList map = new MapList(fromRange, regions, 1, 1);
+ return new GeneLociI()
+ {
+
+ @Override
+ public String getSpeciesId()
+ {
+ return species == null ? "" : species;
+ }
+
+ @Override
+ public String getAssemblyId()
+ {
+ return as;
+ }
+
+ @Override
+ public String getChromosomeId()
+ {
+ return chr;
+ }
+
+ @Override
+ public MapList getMap()
+ {
+ return map;
+ }
+ };
+ } catch (IOException | ParseException | NumberFormatException e)
+ {
+ // ignore
+ }
+
+ return null;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff