Merge branch 'master' of https://github.com/Ensembl/ensembl

misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateBasic.pm

@@ -295,7 +295,10 @@ EON
   my $exe_file = $root_dir."/".$unique_name.".submit";
   open(my $rh,">", $exe_file) || die "Could not open file $exe_file";
   
-  print $rh ". /usr/local/lsf/conf/profile.lsf\n";
+  my $lsf_conf = "/usr/local/lsf/conf/profile.lsf";
+  if (-e $lsf_conf) {
+    print $rh ". $lsf_conf\n";
+  }
   print $rh $command."\n";
 
   close $rh;

misc-scripts/xref_mapping/XrefMapper/wormbase.pm

@@ -77,8 +77,19 @@ sub set_display_xrefs {
     return;
   }
 
+  my $query_gseq_sth =  $self->core->dbc->prepare("SELECT ensembl_id, x.xref_id " .
+                                                 "FROM object_xref ox, xref x ". 
+                                                 "WHERE ox.xref_id = x.xref_id AND external_db_id = " . $external_dbs{wormbase_gseqname});
+  $query_gseq_sth->execute();
+  while( my ($gid, $xid) = $query_gseq_sth->fetchrow_array) {
+    $gene_display_xrefs{$gid} = $xid;
+  }
+  $query_gseq_sth->finish;
+  
+
+
   #
-  # Get the wormbase_locus xrefs for the genes
+  # Some genes will have a locus name. Over-write display xrefs for those that do
   #
   my $query_gene_sth = $self->core->dbc->prepare("SELECT ensembl_id, x.xref_id " .
                                                  "FROM object_xref ox, xref x ". 

misc-scripts/xref_mapping/XrefParser/ArrayExpressParser.pm

@@ -86,48 +86,44 @@ sub run_script {
   #get stable_ids from core and create xrefs 
 
   my $registry = "Bio::EnsEMBL::Registry";
-  my $gene_adaptor;
-  print "Loading the Registry\n" if $verbose;
-  if ($project eq 'ensembl') {
-      if ($host) {
-          my $db = Bio::EnsEMBL::DBSQL::DBAdaptor->new(
-              '-host'     => $host,
-              '-user'     => $user,
-              '-pass'     => $pass,
-              '-dbname'   => $dbname,
-              '-species'  => $species_name,
-              '-group'    => 'core',
-       );
-      $gene_adaptor = $db->get_GeneAdaptor();
-      } else {
-      $registry->load_registry_from_multiple_dbs( 
-	  {
-	      '-host'    => 'ens-staging1',
-	      '-user'    => 'ensro',
-	  },
-          {
-              '-host'     => 'ens-staging2',
-              '-user'     => 'ensro',
-          }
-       );
-       $gene_adaptor = $registry->get_adaptor($species_name, 'core', 'Gene');
-     }
+  my ($gene_adaptor);
+  if ($host) {
+    my $db = Bio::EnsEMBL::DBSQL::DBAdaptor->new(
+      '-host'     => $host,
+      '-user'     => $user,
+      '-pass'     => $pass,
+      '-dbname'   => $dbname,
+      '-species'  => $species_name,
+      '-group'    => 'core',
+        );
+    $gene_adaptor = $db->get_GeneAdaptor();
+  } elsif ($project eq 'ensembl') {
+    print "Loading the Registry\n" if $verbose;
+    $registry->load_registry_from_multiple_dbs( 
+      {
+        '-host'    => 'ens-staging1',
+        '-user'    => 'ensro',
+      },
+      {
+        '-host'     => 'ens-staging2',
+        '-user'     => 'ensro',
+      }
+        );
+    $gene_adaptor = $registry->get_adaptor($species_name, 'core', 'Gene');
   } elsif ($project eq 'ensemblgenomes') {
-
-      $registry->load_registry_from_multiple_dbs( 
-	  {
-	      '-host'     => 'mysql-eg-staging-1.ebi.ac.uk',
-	      '-port'     => 4160,
-	      '-user'     => 'ensro',
-	  },
-	  {
-	      '-host'     => 'mysql-eg-staging-2.ebi.ac.uk',
-	      '-port'     => 4275,
-	      '-user'     => 'ensro',
-	  },
- 
-      );
-      $gene_adaptor = $registry->get_adaptor($species_name, 'core', 'Gene');
+    $registry->load_registry_from_multiple_dbs( 
+      {
+        '-host'     => 'mysql-eg-staging-2.ebi.ac.uk',
+        '-port'     => 4160,
+        '-user'     => 'ensro',
+      },
+      {
+        '-host'     => 'mysql-eg-staging-2.ebi.ac.uk',
+        '-port'     => 4275,
+        '-user'     => 'ensro',
+      },
+        );
+    $gene_adaptor = $registry->get_adaptor($species_name, 'core', 'Gene');
   } else {
       die("Missing or unsupported project value. Supported values: ensembl, ensemblgenomes");
   }

misc-scripts/xref_mapping/xref_config.ini

@@ -4569,6 +4569,17 @@ parser          = comes from WormbaseDirectParser
 release_uri     =
 data_uri        =
 
+[source wormbase_gseqname::wormbase]
+# Used by caenorhabditis_elegans comes from WormbaseDirectParser
+name            = wormbase_gseqname
+download        = N
+order           = 50
+priority        = 1
+prio_descr      =
+parser          = comes from WormbaseDirectParser
+release_uri     =
+data_uri        =
+
 [source wormbase_transcript::caenorhabditis_elegans]
 # Used by caenorhabditis_elegans comes from WormbaseDatabaseStableIDParser
 name            = wormbase_transcript
@@ -5475,16 +5486,15 @@ taxonomy_id     = 6239
 aliases         = caenorhabditiselegans, celegans, elegans
 source          = EntrezGene::MULTI
 source          = GO::caenorhabditis_elegans
-source          = goslim_goa::MULTI
-source          = InterproGO::MULTI
-source          = Interpro::MULTI
+source          = goslim_goa::EG
 source          = RefSeq_dna::caenorhabditis_elegans
 source          = RefSeq_peptide::caenorhabditis_elegans
 source          = UniGene::caenorhabditis_elegans
 source          = Uniprot/SPTREMBL::MULTI
 source          = Uniprot/SWISSPROT::MULTI
+source          = UniParc::MULTI
 source          = wormbase::caenorhabditis_elegans
-source 		= ArrayExpress::MULTI
+source          = ArrayExpress::EG
 
 [species callithrix_jacchus]
 taxonomy_id     = 9483