Merge pull request #234 from WormBase/WBPS17.5

Fixing PARASITE-463
WormBase · Jun 8, 2022 · 02cfed5 · 02cfed5
2 parents 509f866 + 6f7f703
commit 02cfed5
Showing 1 changed file with 65 additions and 82 deletions.
diff --git a/parasite/scripts/production/core-creation/load_synonyms.pl b/parasite/scripts/production/core-creation/load_synonyms.pl
@@ -26,17 +26,17 @@
 my $optsd = [ @{ $cli_helper->get_dba_opts() } ];
 push( @{$optsd}, "file:s" );
 push( @{$optsd}, "verbose" );
-# push( @{$optsd}, "extdb:s" );
+push( @{$optsd}, "extdb:s" );
 
 my $opts = $cli_helper->process_args( $optsd, \&pod2usage );
 
 if( !$opts->{'file'} ){
   die "# need -file synonyms.edited.tsv  NOTE: make sure you edit it before loading!\n";
 }
 
-# if( !$opts->{'extdb'} ){
-#   die "# need -extdb arg, example -extdb EntrezGene\n";
-# }
+if( !$opts->{'extdb'} ){
+  die "# need -extdb arg, example -extdb EntrezGene\n";
+}
 
 if( $opts->{'verbose'} ) {
   Log::Log4perl->easy_init($DEBUG);
@@ -62,7 +62,7 @@
 
 ## SQL statements
 
-my $synonym_store_sth = $dba->dbc->prepare("INSERT INTO 
+my $synonym_store_sth = $dba->dbc->prepare("INSERT INTO
         external_synonym (xref_id, synonym)
         VALUES (?, ?)
         ");
@@ -89,7 +89,7 @@
 
     next if($line =~ m/^#/ || $line !~ m/\t/);
 
-    chomp($line); 
+    chomp($line);
     ($stableid, $synonym) = split(/\t/, $line);
 
     # accumulate synonyms of the same stable_id
@@ -98,93 +98,76 @@
 close(TSV);
 
 
-# ## 3) Check that the external_db exists, and add it if not
-#
-# my $dbname = $opts->{'extdb'};
-# my $dbRefs = $dea->get_external_db_ids($dbname, 'NULL', 1);
-# unless (scalar(@$dbRefs)>0){
-#   $logger->info( "Adding new external_db entry for ", $opts->{'extdb'});
-#   $add_external_db_sth->execute($opts->{'extdb'});
-#   $add_external_db_sth->finish();
-#   $dbRefs = $dea->get_external_db_ids($dbname, 'NULL', 1);
-# }
+## 3) Check that the external_db exists, and add it if not
+
+my $dbname = $opts->{'extdb'};
+my $dbRefs = $dea->get_external_db_ids($dbname, 'NULL', 1);
+unless (scalar(@$dbRefs)>0){
+  $logger->info( "Adding new external_db entry for ", $opts->{'extdb'});
+  $add_external_db_sth->execute($opts->{'extdb'});
+  $add_external_db_sth->finish();
+  $dbRefs = $dea->get_external_db_ids($dbname, 'NULL', 1);
+}
 
 
 ## 4) create display_xrefs linked to synonyms
 
 foreach $stableid (keys(%syns)) {
 
-    # check target gene exists 
-    my $gene = $gene_adaptor->fetch_by_stable_id($stableid);
-    if (!$gene) {
-        $logger->info("Cannot find $stableid, skip it");
+    # check target gene exists
+        my $gene = $gene_adaptor->fetch_by_stable_id($stableid);
+        if ( !$gene ) {
+        $logger->info( "Cannot find $stableid, skip it");
         next;
-    }
+     }
 
     # check whether gene already has display_xref
-    my $old_display_xrefs = $gene->get_all_object_xrefs();
-    my @old_xref_ids = [];
-    foreach my $old_display_xref (@$old_display_xrefs) {
-        my $pid = $old_display_xref->primary_id();
-        my $xid = $old_display_xref->dbID();
-        if ($pid eq $stableid) {
-            push(@old_xref_ids, $old_display_xref)
-        }
-    }
-    my $loa = @old_xref_ids;
-    if ($loa eq 2) {
-        my $old_display_xref = @old_xref_ids[1];
-        $logger->info("$stableid has xref_id set to ", $old_display_xref->display_id());
+      my $old_display_xref = $gene->display_xref();
+
+      if( $old_display_xref ) {
+        $logger->info( "$stableid has display_xref_id set to ", $old_display_xref->display_id() );
         # get its xref_id
-        my $xref_id = $old_display_xref->dbID();
-        $logger->info("Its xref_id is $xref_id");
-        # get existing synonyms for this xref
-        my @existing_synonyms = @{$old_display_xref->get_all_synonyms};
+	my $xref_id = $old_display_xref->dbID();
+        $logger->info( "Its xref_id is $xref_id");
+	# get existing synonyms for this xref
+        my @existing_synonyms = @{$old_display_xref->get_all_synonyms };
         # hang the synonyms off the existing display xref
-        SYN:
-        foreach $synonym (@{$syns{$stableid}}) {
-            # check the synonym isn't already added
-            foreach my $existing_synonym (@existing_synonyms) {
-                if ($synonym eq $existing_synonym) {
-                    $logger->info("$synonym already associated with $stableid, skipping");
-                    next SYN;
-                }
-            }
-            $synonym_store_sth->execute($xref_id, $synonym);
-            $logger->info("Added $synonym to $stableid");
+	SYN: foreach $synonym (@{$syns{$stableid}}){
+	  # check the synonym isn't already added
+	  foreach my $existing_synonym (@existing_synonyms){
+            if ($synonym eq $existing_synonym){
+	      $logger->info( "$synonym already associated with $stableid, skipping");
+	      next SYN;
+	    }
+	  }
+          $synonym_store_sth->execute($xref_id, $synonym);
+	  $logger->info( "Added $synonym to $stableid");
         }
-        $gene->display_xref($old_display_xref);
-        $gene_adaptor->update($gene);
-        $synonym_store_sth->finish();
+	$synonym_store_sth->finish();
     }
 
-    # no existing display_xref so we make a new one to hang the synonyms off
-    # use the stableid as the xref's ID and display label- sorry Ensembl :(
-    else {
-        $logger->info("$stableid doesn't have a curated_gene_synonyms xref. Have you ran Xref pipeline?");
-        die;
-    }
-}
-
-#     else{
-#       my $new_display_xref = Bio::EnsEMBL::DBEntry -> new (
-# 	     -PRIMARY_ID  => $stableid,
-#              -DBNAME      => $opts->{'extdb'},
-#              -DISPLAY_ID  => $stableid,
-#              -INFO_TYPE   => 'SEQUENCE_MATCH',
-#          );
-#       # add all synonyms to the new xref
-#       foreach $synonym (@{$syns{$stableid}}){
-#         $new_display_xref->add_synonym($synonym);
-# 	$logger->info( "Added $synonym to $stableid");
-#       }
-#       $dbRefs = $dea->get_external_db_ids($dbname, 'NULL', 1);
-#       my $dbRef = shift(@$dbRefs);
-#       my $xref_id = $dea->_store_or_fetch_xref($new_display_xref,$dbRef);
-#       $new_display_xref->dbID($xref_id);
-#
-#       # and update the gene
-#       $gene->display_xref($new_display_xref);
-#       $gene_adaptor->update($gene);
-#    }
-# }
+   # no existing display_xref so we make a new one to hang the synonyms off
+   # use the stableid as the xref's ID and display label- sorry Ensembl :(
+
+    else{
+      my $new_display_xref = Bio::EnsEMBL::DBEntry -> new (
+	     -PRIMARY_ID  => $stableid,
+             -DBNAME      => $opts->{'extdb'},
+             -DISPLAY_ID  => $stableid,
+             -INFO_TYPE   => 'SEQUENCE_MATCH',
+         );
+      # add all synonyms to the new xref
+      foreach $synonym (@{$syns{$stableid}}){
+        $new_display_xref->add_synonym($synonym);
+	$logger->info( "Added $synonym to $stableid");
+      }
+      $dbRefs = $dea->get_external_db_ids($dbname, 'NULL', 1);
+      my $dbRef = shift(@$dbRefs);
+      my $xref_id = $dea->_store_or_fetch_xref($new_display_xref,$dbRef);
+      $new_display_xref->dbID($xref_id);
+
+      # and update the gene
+      $gene->display_xref($new_display_xref);
+      $gene_adaptor->update($gene);
+   }
+}