Added a script to load a chosen display id for each gene and transcript

misc-scripts/protein_match/load_transcript_display_id.pl

+#Contact: Emmanuel Mongin (mongin@ebi.ac.uk)
+
+use strict;
+use DBI;
+use Getopt::Long;
+use Bio::EnsEMBL::DBSQL::DBAdaptor;
+use Bio::EnsEMBL::DBSQL::DBEntryAdaptor;
+use Bio::EnsEMBL::DBEntry;
+use Bio::SeqIO;
+#use MultiTestDB;
+
+
+BEGIN {
+    my $script_dir = $0;
+    $script_dir =~ s/(\S+\/)\S+/$1/;
+    unshift (@INC, $script_dir);
+    require "mapping_conf.pl";
+}
+
+my %conf =  %::mapping_conf; # configuration options
+
+
+# global vars
+
+
+my $dbname     = $conf{'db'};
+my $host       = $conf{'host'};
+my $user       = $conf{'dbuser'};
+my $pass       = $conf{'password'};
+my $organism   = $conf{'organism'};
+my %priority;
+
+$priority{'HUGO'} = 1000;
+$priority{'MarkerSymbol'} = 1000;
+$priority{'SWISSPROT'} = 900;
+$priority{'SPTREMBL'} = 800;
+$priority{'RefSeq'} = 600;
+
+if (!defined $organism) {
+    die "\nSome basic options have not been set up, have a look at mapping_conf\nCurrent set up (required options):\norganism: $organism\n\n";
+}
+
+print STDERR "Connecting to the database...\n";
+
+#my $multi = MultiTestDB->new();
+
+my $db = Bio::EnsEMBL::DBSQL::DBAdaptor->new(
+        -user   => $user,
+        -dbname => $dbname,
+        -host   => $host,
+	-pass   => $pass,			     
+        -driver => 'mysql',
+	);
+
+#my $db = $multi->get_DBAdaptor( 'core' );
+
+my $transadaptor = $db->get_TranscriptAdaptor();
+my $geneadaptor  = $db->get_GeneAdaptor();
+my $xrefadaptor  = $db->get_DBEntryAdaptor();
+
+my $query = "select transcript_id from transcript";
+my $sth = $db->prepare($query);
+$sth->execute();
+
+while(my $id = $sth->fetchrow) {
+    my $trans = $transadaptor->fetch_by_dbID($id);
+    my $xrefs = $trans->get_all_DBLinks;
+    my $display;
+    my $current = 0;
+    foreach my $xref(@$xrefs) {
+	if ($priority{$xref->database} > $current) {
+	    $display = $xref->dbID;
+	}
+    }
+    $trans->display_xref($display);
+    $transadaptor->update($trans);
+    #print STDERR "ID: $id\tDISPLAY: $display\tTEST: ".$transadaptor->get_display_xref_id($id)."\n";
+}
+
+my $query1 = "select gene_id from gene";
+my $sth1 = $db->prepare($query1);
+$sth1->execute();
+
+while(my $gene_id = $sth1->fetchrow) {
+    my $gene = $geneadaptor->fetch_by_dbID($gene_id);
+    my $transcripts = $gene->get_all_Transcripts();
+    my $display;
+    my $current;
+    foreach my $trans(@$transcripts) {
+	my $id = $trans->dbID();
+	my $xrefid = $transadaptor->get_display_xref_id($id);
+	
+	eval {
+	    my $xref = $xrefadaptor->fetch_by_dbID($xrefid);
+	    if ($priority{$xref->database} > $current) {
+		$display = $xref->dbID;
+	    }
+	};
+    }
+    $gene->display_xref($display);
+    $geneadaptor->update($gene);
+#    print STDERR "GENE_ID: $gene_id\tDISPLAY: $display\tTEST: ".$geneadaptor->get_display_xref_id($gene_id)."\n";
+}