diff --git a/misc-scripts/ontology/scripts/demo1.pl b/misc-scripts/ontology/scripts/demo1.pl index 8a25e8e07a7c744af3effc0028b10436719f9d3b..902efc068b053c3959334e0d0be9a6277a46c639 100755 --- a/misc-scripts/ontology/scripts/demo1.pl +++ b/misc-scripts/ontology/scripts/demo1.pl @@ -16,16 +16,25 @@ use Bio::EnsEMBL::Registry; my $registry = 'Bio::EnsEMBL::Registry'; +<<<<<<< demo1.pl +$registry->load_registry_from_db( + '-host' => 'ens-staging', + '-user' => 'ensro', + '-db_version' => 56, + '-verbose' => 1, +); +======= $registry->load_registry_from_db( '-host' => 'ensembldb.ensembl.org', '-user' => 'anonymous' ); +>>>>>>> 1.4 -my $accession = 'GO:0030326'; +my $accession = 'GO:0050825'; # Get a GO term adaptor and a gene adaptor (for human). my $go_adaptor = $registry->get_adaptor( 'Multi', 'Ontology', 'GOTerm' ); -my $gene_adaptor = $registry->get_adaptor( 'Human', 'Core', 'Gene' ); +my $gene_adaptor = $registry->get_adaptor( 'Mouse', 'Core', 'Gene' ); # Fetch a GO term by its accession. my $term = $go_adaptor->fetch_by_accession($accession); diff --git a/misc-scripts/ontology/scripts/load_OBO_file.pl b/misc-scripts/ontology/scripts/load_OBO_file.pl index 5db40eb2631b5235685cc456cd53fc6778d99f60..806230c1747355ab13d16a65f832be35df74e425 100755 --- a/misc-scripts/ontology/scripts/load_OBO_file.pl +++ b/misc-scripts/ontology/scripts/load_OBO_file.pl @@ -431,12 +431,11 @@ EOT my $type = $1; my $data = $2; - if ( $type eq 'id' ) { $term{'accession'} = $data } - elsif ( $type eq 'name' ) { $term{'name'} = $data } - elsif ( $type eq 'namespace' ) { $term{'namespace'} = $data } - elsif ( $type eq 'def' ) { - ( $term{'definition'} ) = $data =~ /"([^"]+)"/; - } elsif ( $type eq 'is_a' ) { + if ( $type eq 'id' ) { $term{'accession'} = $data } + elsif ( $type eq 'name' ) { $term{'name'} = $data } + elsif ( $type eq 'namespace' ) { $term{'namespace'} = $data } + elsif ( $type eq 'def' ) { $term{'definition'} = $data } + elsif ( $type eq 'is_a' ) { my ($parent_acc) = $data =~ /(\S+)/; push( @{ $term{'parents'}{'is_a'} }, $parent_acc ); } elsif ( $type eq 'relationship' ) {