X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblMap.java;h=56657e0578c517e8c02717e1d57060a77a557f70;hb=353109c11d706b29ae5bc9606f0e12223aa45a98;hp=05cc8977701c2293a1e792e8ae5949547d7990da;hpb=e464da0ea20b0322846ce623598a16f2a1cba7ae;p=jalview.git diff --git a/src/jalview/ext/ensembl/EnsemblMap.java b/src/jalview/ext/ensembl/EnsemblMap.java index 05cc897..56657e0 100644 --- a/src/jalview/ext/ensembl/EnsemblMap.java +++ b/src/jalview/ext/ensembl/EnsemblMap.java @@ -2,11 +2,15 @@ package jalview.ext.ensembl; 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; @@ -17,6 +21,13 @@ import org.json.simple.parser.ParseException; public class EnsemblMap extends EnsemblRestClient { + private static final String MAPPED = "mapped"; + + 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) @@ -62,7 +73,7 @@ public class EnsemblMap extends EnsemblRestClient * @return * @throws MalformedURLException */ - protected URL getUrl(String species, String chromosome, String fromRef, + protected URL getAssemblyMapUrl(String species, String chromosome, String fromRef, String toRef, int startPos, int endPos) throws MalformedURLException { @@ -77,13 +88,7 @@ public class EnsemblMap extends EnsemblRestClient "%s/map/%s/%s/%s:%d..%d:%s/%s?content-type=application/json", getDomain(), species, fromRef, chromosome, start, end, strand, toRef); - try - { - return new URL(url); - } catch (MalformedURLException e) - { - return null; - } + return new URL(url); } @Override @@ -110,7 +115,19 @@ public class EnsemblMap extends EnsemblRestClient return null; // not used } - public int[] getMapping(String species, String chromosome, + /** + * Calls the REST /map service to get the chromosomal coordinates (start/end) + * in 'toRef' that corresponding to the (start/end) queryRange in 'fromRef' + * + * @param species + * @param chromosome + * @param fromRef + * @param toRef + * @param queryRange + * @return + * @see http://rest.ensemblgenomes.org/documentation/info/assembly_map + */ + public int[] getAssemblyMapping(String species, String chromosome, String fromRef, String toRef, int[] queryRange) { URL url = null; @@ -118,21 +135,32 @@ public class EnsemblMap extends EnsemblRestClient try { - url = getUrl(species, chromosome, fromRef, toRef, queryRange[0], + url = getAssemblyMapUrl(species, chromosome, fromRef, toRef, queryRange[0], queryRange[1]); - // System.out.println("Calling " + url); br = getHttpResponse(url, null); - return (parseResponse(br)); + return (parseAssemblyMappingResponse(br)); } catch (Throwable t) { System.out.println("Error calling " + url + ": " + t.getMessage()); return null; + } finally + { + if (br != null) + { + try + { + br.close(); + } catch (IOException e) + { + // ignore + } + } } } /** - * Parses the JSON response from the /map REST service. The format is (with - * some fields omitted) + * Parses the JSON response from the /map/<species>/ REST service. The + * format is (with some fields omitted) * *
* {"mappings": @@ -145,7 +173,7 @@ public class EnsemblMap extends EnsemblRestClient * @param br * @return */ - protected int[] parseResponse(BufferedReader br) + protected int[] parseAssemblyMappingResponse(BufferedReader br) { int[] result = null; JSONParser jp = new JSONParser(); @@ -153,14 +181,14 @@ public class EnsemblMap extends EnsemblRestClient try { JSONObject parsed = (JSONObject) jp.parse(br); - JSONArray mappings = (JSONArray) parsed.get("mappings"); + JSONArray mappings = (JSONArray) parsed.get(MAPPINGS); Iterator rvals = mappings.iterator(); while (rvals.hasNext()) { // todo check for "mapped" JSONObject val = (JSONObject) rvals.next(); - JSONObject mapped = (JSONObject) val.get("mapped"); + JSONObject mapped = (JSONObject) val.get(MAPPED); int start = Integer.parseInt(mapped.get("start").toString()); int end = Integer.parseInt(mapped.get("end").toString()); String strand = mapped.get("strand").toString(); @@ -180,4 +208,215 @@ public class EnsemblMap extends EnsemblRestClient return result; } + /** + * 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); + 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/or /map/cdna/ REST service. The + * REST call is to either ensembl or ensemblgenomes, as determined from the + * division, e.g. Ensembl or EnsemblProtists. + * + * @param domain + * @param accession + * @param start + * @param end + * @param cdsOrCdna + * @return + * @throws MalformedURLException + */ + URL getIdMapUrl(String domain, String accession, int start, int end, + String cdsOrCdna) throws MalformedURLException + { + String url = String + .format("%s/map/%s/%s/%d..%d?include_original_region=1&content-type=application/json", + domain, cdsOrCdna, accession, start, end); + return new URL(url); + } + + /** + * Parses the JSON response from the /map/cds/ or /map/cdna REST service. The + * format is + * + * + * {"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} + * ] + * } + *+ * + * @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; + Listregions = 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 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; + } + }