JAL-2743 look up species and gene loci for Ensembl gene

diff --git a/src/jalview/ext/ensembl/EnsemblGene.java b/src/jalview/ext/ensembl/EnsemblGene.java
index afff4c2..11322c8 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblGene.java
+++ b/src/jalview/ext/ensembl/EnsemblGene.java
@@ -147,10 +147,9 @@ public class EnsemblGene extends EnsemblSeqProxy
         continue;
       }
       
-      parseChromosomeLocations(geneAlignment);
-      
       if (geneAlignment.getHeight() == 1)
       {
+        findGeneLoci(geneAlignment.getSequenceAt(0), geneId);
         getTranscripts(geneAlignment, geneId);
       }
       if (al == null)
@@ -166,42 +165,64 @@ public class EnsemblGene extends EnsemblSeqProxy
   }
 
   /**
+   * Calls the /lookup/id REST service, parses the response for gene
+   * coordinates, and if successful, adds these to the sequence
+   * 
+   * @param seq
+   * @param geneId
+   */
+  void findGeneLoci(SequenceI seq, String geneId)
+  {
+    /*
+     * if sequence description is in gene loci format, parse this
+     * - but try remote lookup anyway as 'better' if available
+     */
+    parseChromosomeLocations(seq);
+
+    GeneLociI geneLoci = new EnsemblLookup(getDomain()).getGeneLoci(geneId);
+    if (geneLoci != null)
+    {
+      seq.setGeneLoci(geneLoci.getSpeciesId(), geneLoci.getAssemblyId(),
+              geneLoci.getChromosomeId(), geneLoci.getMap());
+    }
+  }
+
+  /**
    * Parses and saves fields of an Ensembl-style description e.g.
    * chromosome:GRCh38:17:45051610:45109016:1
    * 
-   * @param alignment
+   * @param seq
    */
-  private void parseChromosomeLocations(AlignmentI alignment)
+  boolean parseChromosomeLocations(SequenceI seq)
   {
-    for (SequenceI seq : alignment.getSequences())
+    String description = seq.getDescription();
+    if (description == null)
+    {
+      return false;
+    }
+    String[] tokens = description.split(":");
+    if (tokens.length == 6 && tokens[0].startsWith(DBRefEntry.CHROMOSOME))
     {
-      String description = seq.getDescription();
-      if (description == null)
+      String ref = tokens[1];
+      String chrom = tokens[2];
+      try
       {
-        continue;
-      }
-      String[] tokens = description.split(":");
-      if (tokens.length == 6 && tokens[0].startsWith(DBRefEntry.CHROMOSOME))
+        int chStart = Integer.parseInt(tokens[3]);
+        int chEnd = Integer.parseInt(tokens[4]);
+        boolean forwardStrand = "1".equals(tokens[5]);
+        String species = ""; // not known here
+        int[] from = new int[] { seq.getStart(), seq.getEnd() };
+        int[] to = new int[] { forwardStrand ? chStart : chEnd,
+            forwardStrand ? chEnd : chStart };
+        MapList map = new MapList(from, to, 1, 1);
+        seq.setGeneLoci(species, ref, chrom, map);
+        return true;
+      } catch (NumberFormatException e)
       {
-        String ref = tokens[1];
-        String chrom = tokens[2];
-        try
-        {
-          int chStart = Integer.parseInt(tokens[3]);
-          int chEnd = Integer.parseInt(tokens[4]);
-          boolean forwardStrand = "1".equals(tokens[5]);
-          String species = ""; // dunno yet!
-          int[] from = new int[] { seq.getStart(), seq.getEnd() };
-          int[] to = new int[] { forwardStrand ? chStart : chEnd,
-              forwardStrand ? chEnd : chStart };
-          MapList map = new MapList(from, to, 1, 1);
-          seq.setGeneLoci(species, ref, chrom, map);
-        } catch (NumberFormatException e)
-        {
-          System.err.println("Bad integers in description " + description);
-        }
+        System.err.println("Bad integers in description " + description);
       }
     }
+    return false;
   }
 
   /**

diff --git a/src/jalview/ext/ensembl/EnsemblLookup.java b/src/jalview/ext/ensembl/EnsemblLookup.java
index 5a616f0..0d1b554 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblLookup.java
+++ b/src/jalview/ext/ensembl/EnsemblLookup.java
@@ -20,13 +20,17 @@
  */
 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;
 
@@ -137,7 +141,7 @@ public class EnsemblLookup extends EnsemblRestClient
    */
   public String getGeneId(String identifier)
   {
-    return getResult(identifier, br -> parseGeneId(br));
+    return (String) getResult(identifier, br -> parseGeneId(br));
   }
 
   /**
@@ -149,7 +153,7 @@ public class EnsemblLookup extends EnsemblRestClient
    */
   public String getSpecies(String identifier)
   {
-    return getResult(identifier, br -> getAttribute(br, SPECIES));
+    return (String) getResult(identifier, br -> getAttribute(br, SPECIES));
   }
 
   /**
@@ -160,8 +164,8 @@ public class EnsemblLookup extends EnsemblRestClient
    * @param parser
    * @return
    */
-  protected String getResult(String identifier,
-          Function<BufferedReader, String> parser)
+  protected Object getResult(String identifier,
+          Function<BufferedReader, Object> parser)
   {
     List<String> ids = Arrays.asList(new String[] { identifier });
 
@@ -265,4 +269,80 @@ public class EnsemblLookup extends EnsemblRestClient
     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, 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());
+    }
+    return null;
+  }
+
 }