Commit cae15912 authored by Ian Longden's avatar Ian Longden
Browse files

Move all to Genes. Die if external_db_id is not defined

parent b077f0ae
......@@ -77,6 +77,7 @@ sub run_coordinatemapping {
$sth_stat->finish;
return;
}
print "species = $species ($species_id))\n";
my $output_dir = $core_db->dir();
......@@ -208,18 +209,13 @@ 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,
......@@ -231,6 +227,10 @@ sub run_coordinatemapping {
}
$xref_sth->finish();
if(!defined($external_db_id)){
die "External_db_id is undefined species_id = $species_id\n";
}
######################################################################
# Do coordinate matching. #
######################################################################
......@@ -602,6 +602,9 @@ sub run_coordinatemapping {
$sth_stat = $self->xref->dbc->prepare("insert into process_status (status, date) values('coordinate_xref_finished',now())");
$sth_stat->execute();
$sth_stat->finish;
$self->biomart_fix("UCSC","Translation","Gene");
$self->biomart_fix("UCSC","Transcript","Gene");
} ## end sub run_coordinatemapping
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment