Assign projected xrefs to genes, transcripts or translations depending on what...

Assign projected xrefs to genes, transcripts or translations depending on what type of object other xrefs of this type are assigned to.

misc-scripts/xref_projection/project_display_xrefs.pl

@@ -64,6 +64,9 @@ foreach my $to_species (@to_multi) {
 
   my $mlss = $mlssa->fetch_by_method_link_type_registry_aliases($method_link_type, [$from_species, $to_species]);
 
+  # build hash of external db name -> ensembl object type mappings
+  my %db_to_type = build_db_to_type($to_ga);
+
   print "$to_species, before projection: \n" . &get_stats($to_ga);
 
   # Get all genes, find homologies, set xrefs
@@ -78,7 +81,7 @@ foreach my $to_species (@to_multi) {
 
     my $homologies = $ha->fetch_all_by_Member_MethodLinkSpeciesSet($member, $mlss);
 
-    project_homologies($homologies, $to_ga, $to_dbea, $names, $go_terms, $ma);
+    project_homologies($homologies, $to_ga, $to_dbea, $names, $go_terms, $ma, %db_to_type);
 
   }
 
@@ -91,7 +94,7 @@ foreach my $to_species (@to_multi) {
 # Project homologies from first to subsequent species
 sub project_homologies() {
 
-  my ($homologies, $to_ga, $to_dbea, $names, $go_terms, $ma) = @_;
+  my ($homologies, $to_ga, $to_dbea, $names, $go_terms, $ma, %db_to_type) = @_;
 
   foreach my $homology (@{$homologies}) {
 
@@ -102,7 +105,7 @@ sub project_homologies() {
     # ----------------------------------------
     # Display names and descriptions
 
-    project_display_names($to_ga, $to_dbea, $ma, $from_member, $to_member) if ($names);
+    project_display_names($to_ga, $to_dbea, $ma, $from_member, $to_member, %db_to_type) if ($names);
 
     # ----------------------------------------
     # GO terms
@@ -120,7 +123,7 @@ sub project_homologies() {
 
 sub project_display_names {
 
-  my ($to_ga, $to_dbea, $ma, $from_member, $to_member) = @_;
+  my ($to_ga, $to_dbea, $ma, $from_member, $to_member, %db_to_type) = @_;
 
   my $to_gene = $to_ga->fetch_by_stable_id($to_member->stable_id());
 
@@ -138,19 +141,51 @@ sub project_display_names {
       my $txt = " [from $from_species gene " . $from_gene->stable_id() . "]";
       $dbEntry->display_id($dbEntry->display_id() . $txt);
 
-      # Add the xref to the "to" gene, set its status to "KNOWN", modify the description and update display_xref
-      $to_gene->add_DBEntry($dbEntry);
+      # Add the xref to the "to" gene, or transcript or translation depending on what the
+      # other xrefs from this dbname as assigned to (see build_db_to_type)
+      # Note that if type is not found, it means that we're dealing with a db that has no
+      # xrefs in the target database, e.g. MarkerSymbol in mouse -> rat
+      # In this case just assign to transcripts
+
+      my @to_transcripts = @{$to_gene->get_all_Transcripts};
+      my $to_transcript = $to_transcripts[0];
+
+      my $type = $db_to_type{$dbEntry->dbname()};
+
+      if ($type eq "Gene") {
+
+	$to_gene->add_DBEntry($dbEntry);
+	$to_dbea->store($dbEntry, $to_gene, 'Gene') if (!$print);
+
+      } elsif ($type eq "Transcript" || !$type) {
+	
+	$to_transcript->add_DBEntry($dbEntry);
+	$to_dbea->store($dbEntry, $to_transcript, 'Transcript') if (!$print);
+
+      } elsif ($type eq "Translation") {
+
+	my $to_translation = $to_transcript->translation();
+	return if ($to_translation);
+	$to_translation->add_DBEntry($dbEntry);
+	$to_dbea->store($dbEntry, $to_translation, 'Translation') if (!$print);
+
+      } else {
+
+	warn("Can't deal with xrefs assigned to $type (dbname=" . $dbEntry->dbname . ")\n");
+	return;
+
+      }
+
+      # Set gene status to "KNOWN", modify the description and update display_xref
+
       $to_gene->status("KNOWN");
       $to_gene->description($from_gene->description() . $txt) if ($from_gene->description());
       $to_gene->display_xref($dbEntry);
 	
       print $to_gene->stable_id() . " --> " . $dbEntry->display_id() . "\n" if ($print);
 
-      # store - need to add the DBEntry and also update the gene display xref id
-      if (!$print) {
-	$to_dbea->store($dbEntry, $to_gene, 'Gene');
-	$to_ga->update($to_gene);
-      }
+      # update the gene so that the display_xref_id is set
+      $to_ga->update($to_gene) if (!$print);
 
     }
 
@@ -267,6 +302,30 @@ sub count_rows {
 
 # ----------------------------------------------------------------------
 
+# create a hash of external_db_name -> ensembl_object_type
+# used to assign projected xrefs to the "correct" type
+
+sub build_db_to_type {
+
+  my ($to_ga) = @_;
+
+  my %db_to_type = ();
+
+  my $sth = $to_ga->dbc()->prepare("SELECT DISTINCT e.db_name, ox.ensembl_object_type FROM external_db e, xref x, object_xref ox WHERE x.xref_id=ox.xref_id AND e.external_db_id=x.external_db_id");
+  $sth->execute();
+  my ($db_name, $type);
+  $sth->bind_columns(\$db_name, \$type);
+  while($sth->fetch()){
+    $db_to_type{$db_name} = $type;
+  }
+  $sth->finish;
+
+  return %db_to_type;
+
+}
+
+# ----------------------------------------------------------------------
+
 sub usage {
 
   print << "EOF";