name change for source havana -> vega

misc-scripts/xref_mapping/XrefParser/HGNC_ENSTParser.pm

@@ -15,7 +15,12 @@ my $reg = "Bio::EnsEMBL::Registry";
 
 sub run_script {
 
-  my ($self, $file, $source_id, $species_id, $verbose) = @_;
+  my $self = shift if (defined(caller(1)));
+
+  my $file = shift;
+  my $source_id = shift;
+  my $species_id = shift;
+  my $verbose = shift;
 
   my ($type, $my_args) = split(/:/,$file);
 
@@ -38,12 +43,18 @@ sub run_script {
   if($my_args =~ /vhost[=][>](\S+?)[,]/){
     $vhost = $1;
   }
+  if($my_args =~ /vuser[=][>](\S+?)[,]/){
+    $vuser = $1;
+  }
   if($my_args =~ /vport[=][>](\S+?)[,]/){
     $vport =  $1;
   }
   if($my_args =~ /vdbname[=][>](\S+?)[,]/){
     $vdbname = $1;
   }
+  else{
+    print "No vdbname??? $my_args??\n";
+  }	
   if($my_args =~ /vpass[=][>](\S+?)[,]/){
     $vpass = $1;
   }
@@ -57,6 +68,9 @@ sub run_script {
   if($my_args =~ /chost[=][>](\S+?)[,]/){
     $chost = $1;
   }
+  if($my_args =~ /cuser[=][>](\S+?)[,]/){
+    $cuser = $1;
+  }
   if($my_args =~ /cport[=][>](\S+?)[,]/){
     $cport =  $1;
   }
@@ -69,7 +83,7 @@ sub run_script {
   my $vega_dbc;
   my $core_dbc;
   if(defined($vdbname)){
-    print "Using $host $vdbname for Vega and cdbname for Core\n";
+    print "Using $host $vdbname for Vega and $cdbname for Core\n";
     $vega_dbc = $self->dbi2($vhost, $vport, $vuser, $vdbname, $vpass);
     if(!defined($vega_dbc)){
       print "Problem could not open connectipn to $vhost, $vport, $vuser, $vdbname, $vpass\n";
@@ -103,7 +117,7 @@ sub run_script {
 
 
 
-  $source_id = XrefParser::BaseParser->get_source_id_for_source_name("HGNC","havana");
+  $source_id = XrefParser::BaseParser->get_source_id_for_source_name("HGNC","vega");
 
 
   my $sql = 'select tsi.stable_id, x.display_label from xref x, object_xref ox , transcript_stable_id tsi, external_db e where e.external_db_id = x.external_db_id and x.xref_id = ox.xref_id and tsi.transcript_id = ox.ensembl_id and e.db_name like ?';