diff --git a/misc-scripts/xref_mapping/XrefMapper/CoordinateMapper.pm b/misc-scripts/xref_mapping/XrefMapper/CoordinateMapper.pm index da12b149631ac17e48fc4c365167ab03ab438217..9095cbfa7b5bbcc88c0330b86495fe333e034bfc 100644 --- a/misc-scripts/xref_mapping/XrefMapper/CoordinateMapper.pm +++ b/misc-scripts/xref_mapping/XrefMapper/CoordinateMapper.pm @@ -1,9 +1,9 @@ package XrefMapper::CoordinateMapper; -use vars '@ISA'; -@ISA = qw{ XrefMapper::BasicMapper }; +#use vars '@ISA'; +#@ISA = qw{ XrefMapper::BasicMapper }; -use XrefMapper::BasicMapper; +#use XrefMapper::BasicMapper; # $Id$ @@ -22,7 +22,7 @@ use IO::File; use File::Spec::Functions; -use base qw( Exporter ); +use base qw( Exporter XrefMapper::BasicMapper); our @EXPORT = qw( run_coordinatemapping ); @@ -55,7 +55,7 @@ sub mapper{ sub run_coordinatemapping { - my ( $self, $do_upload ) = @_; + my ( $self, $do_upload) = @_; my $sth_stat = $self->xref->dbc->prepare("insert into process_status (status, date) values('coordinate_xrefs_started',now())"); @@ -66,8 +66,8 @@ sub run_coordinatemapping { my $core_db = $self->core(); my $species = $core_db->species(); - my $species_id = $self->mapper->species_id; -# XrefMapper::BasicMapper::get_species_id_from_species_name( $xref_db, $species ); +# my $species_id = $self->mapper->core->species; + my $species_id = XrefMapper::BasicMapper::get_species_id_from_species_name( $xref_db, $species ); # We only do coordinate mapping for mouse and human for now. @@ -208,11 +208,18 @@ sub run_coordinatemapping { $xref_sth->execute($species_id); my $external_db_id; + my $i=0; while ( my $xref = $xref_sth->fetchrow_hashref() ) { $external_db_id ||= $XrefMapper::BasicMapper::source_to_external_db{ $xref->{ 'source_id'} }; $external_db_id ||= 11000; # FIXME (11000 is 'UCSC') + + if($i <20){ + print "ext $external_db_id\n"; + $i++; + } + $unmapped{ $xref->{'coord_xref_id'} } = { 'external_db_id' => $external_db_id,