diff --git a/misc-scripts/xref_mapping/XrefParser/curated_transcriptParser.pm b/misc-scripts/xref_mapping/XrefParser/curated_transcriptParser.pm index 04a32d46f9bca8f6d13386c27e7b8cfd05d09381..53b37e4fb1031a8b35e4b462655804ea74413412 100644 --- a/misc-scripts/xref_mapping/XrefParser/curated_transcriptParser.pm +++ b/misc-scripts/xref_mapping/XrefParser/curated_transcriptParser.pm @@ -91,7 +91,7 @@ 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 $vhost $vdbname for Vega\n"; my $vega_db = XrefParser::Database->new({ host => $vhost, port => $vport, @@ -104,7 +104,21 @@ sub run_script { print "Problem could not open connection to $vhost, $vport, $vuser, $vdbname, $vpass\n"; return 1; } + } else { + $reg->load_registry_from_db( + -host => $host, + -user => $user, + -species => $species_name); + + $vega_dbc = $reg->get_adaptor($species_name,"vega","slice"); + if(!defined($vega_dbc)){ + print "Could not connect to $species_name vega database using load_registry_from_db $host $user\n"; + return 1; + } + $vega_dbc = $vega_dbc->dbc; + } + if (defined($cdbname)){ my $core_db = XrefParser::Database->new({ host => $chost, port => $cport, user => $cuser, @@ -115,21 +129,12 @@ sub run_script { print "Problem could not open connectipn to $chost, $cport, $cuser, $cdbname, $cpass\n"; return 1; } - - } - else{ - + } else{ $reg->load_registry_from_db( -host => $host, -user => $user, -species => $species_name); - $vega_dbc = $reg->get_adaptor($species_name,"vega","slice"); - if(!defined($vega_dbc)){ - print "Could not connect to $species_name vega database using load_registry_from_db $host $user\n"; - return 1; - } - $vega_dbc = $vega_dbc->dbc; $core_dbc = $reg->get_adaptor($species_name,"core","slice"); if(!defined($core_dbc)){ print "Could not connect to $species_name core database using load_registry_from_db $host $user\n";