Commit e4c6cefa authored by Ian Longden's avatar Ian Longden
Browse files

name change for source havana -> vega

parent 4f8506fc
......@@ -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 ?';
......
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