Added options to specify details for connecting to a DNA DB. If your source

(gene) DB contains no DNA, script will throw because it won't be able to
check the translation of transcripts later.

Also print gene stable IDs only when they are present.

misc-scripts/canonical_transcripts/set_canonical_transcripts.pl

@@ -65,6 +65,9 @@ my $port;
 my $dbname;
 my $user;
 my $pass;
+my $dnahost;
+my $dnadbname;
+my $dnauser;
 my $coord_system;
 my $seq_region_name;
 my $write = 0;
@@ -76,6 +79,9 @@ GetOptions( 'dbhost:s'            => \$host,
             'dbname:s'            => \$dbname,
             'dbuser:s'            => \$user,
             'dbpass:s'            => \$pass,
+            'dnahost:s'         => \$dnahost,
+            'dnadbname:s'         => \$dnadbname,
+            'dnauser:s'           => \$dnauser,
             'coord_system_name:s' => \$coord_system,
             'seq_region_name:s'   => \$seq_region_name,
             'write!'              => \$write,
@@ -95,6 +101,21 @@ my $db =
                                       -pass   => $pass );
 
 
+my $geneDB_has_DNA = check_if_DB_contains_DNA($db);
+my $dnadb;
+
+if ($geneDB_has_DNA == 0 && !$dnadbname) {
+  throw ("Your gene DB contains no DNA. You must provide a DNA_DB to connect to");
+} elsif ($geneDB_has_DNA == 0 && $dnadbname) {
+  $dnadb = new Bio::EnsEMBL::DBSQL::DBAdaptor(
+                                                 '-host'   => $dnahost,
+                                                 '-user'   => $dnauser,
+                                                 '-dbname' => $dnadbname,
+                                                 '-port'   => $port,
+                                             );
+  $db->dnadb($dnadb);
+}
+
 my $sa = $db->get_SliceAdaptor;
 my $dea = $db->get_DBEntryAdaptor;
 my $slices;
@@ -118,7 +139,11 @@ SLICE: foreach my $slice (@$slices) {
   my %canonical;
 
 GENE: foreach my $gene (@$genes) {
-    print "Looking at gene: (" . $gene->dbID . ") :: " . $gene->stable_id . "\n";
+    print "Looking at gene: (dbID " . $gene->dbID . ")";
+    if ($gene->stable_id) {
+      print " :: " . $gene->stable_id ;
+    }
+    print "\n";
     my $transcripts = $gene->get_all_Transcripts;
     if ( @$transcripts == 1 ) {
       $canonical{ $gene->dbID } = $transcripts->[0]->dbID;
@@ -271,3 +296,21 @@ GENE: foreach my $gene (@$genes) {
   }
 } ## end foreach my $slice (@$slices)
 
+
+sub check_if_DB_contains_DNA {
+  my ($db) = @_;
+  my $sql_command = "select count(*) from dna";
+  my $sth = $db->dbc->prepare($sql_command);
+  $sth->execute();
+  my @dna_array = $sth->fetchrow_array;
+  if ($dna_array[0] > 0) {
+    print "Your DB ". $db->dbc->dbname ." contains DNA sequences. No need to attach a ".
+          "DNA_DB to it.\n" if ($verbose);
+    return 1;
+  } else {
+    print "Your DB ". $db->dbc->dbname ." does not contain DNA sequences.\n"
+          if ($verbose);
+    return 0;
+  }
+}
+