Added ability to project gene descriptions as well as names etc. Projected...

Added ability to project gene descriptions as well as names etc. Projected descriptions are currently stored the 'old' way, i.e. in the actual gene description field rather than in the info_* fields in the xref table.

misc-scripts/xref_projection/project_display_xrefs.pl

@@ -11,7 +11,7 @@ use Bio::EnsEMBL::DBSQL::GeneAdaptor;
 
 my $method_link_type = "ENSEMBL_HOMOLOGUES";
 
-my ($conf, $compara, $from_species, @to_multi, $print, $names, $go_terms, $delete_names, $delete_go_terms, $no_backup, $full_stats);
+my ($conf, $compara, $from_species, @to_multi, $print, $names, $go_terms, $delete_names, $delete_go_terms, $no_backup, $full_stats, $descriptions);
 
 GetOptions('conf=s'          => \$conf,
 	   'compara=s'       => \$compara,
@@ -25,6 +25,7 @@ GetOptions('conf=s'          => \$conf,
 	   'delete_go_terms' => \$delete_go_terms,
 	   'nobackup'        => \$no_backup,
 	   'full_stats'      => \$full_stats,
+           'descriptions'    => \$descriptions,
 	   'help'            => sub { usage(); exit(0); });
 
 
@@ -83,7 +84,6 @@ foreach my $to_species (@to_multi) {
   print_stats($to_ga);
 
   # Get all genes, find homologies, set xrefs
-
   foreach my $gene_id (@{$from_ga->list_dbIDs}) {
 
     my $gene = $from_ga->fetch_by_dbID($gene_id);
@@ -170,6 +170,11 @@ sub project_display_names {
       # Modify the dbEntry to indicate it's not from this species - set info_type & info_text
       my $txt = "from $from_latin_species gene " . $from_gene->stable_id();
 
+      # Add description to the gene if required
+      # This should probably be in another column in the xref table but we just use the gene
+      # description column for now. 
+      $to_gene->description($from_gene->description()) if ($descriptions && $from_gene->description());
+
       $dbEntry->info_type("PROJECTION");
       $dbEntry->info_text($txt);
 
@@ -508,6 +513,10 @@ sub usage {
 
   [--delete_go_terms]   Delete projected GO terms.
 
+  [--descriptions]      Project descriptions as well. Only works if -names is
+                        specified. Descriptions appended to info_text field,
+                        separated by |
+
   [--print]             Print details of projection only, don't store in database
 
   [--method]            Type of homologs (default: TREE_HOMOLOGIES)