diff --git a/misc-scripts/xref_mapping/XrefParser/HGNC_ENSTParser.pm b/misc-scripts/xref_mapping/XrefParser/HGNC_ENSTParser.pm index 3e7dc86d6f61bb1ecccb7b18ec949fd0dd322f9b..044b604bb7e983080b00d2b00d49a8367a437811 100644 --- a/misc-scripts/xref_mapping/XrefParser/HGNC_ENSTParser.pm +++ b/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 ?';