Commit 58be8878 authored by Tiago Grego's avatar Tiago Grego
Browse files

tab removal, biotype bug

parent 58cf80a6
......@@ -40,36 +40,37 @@ use Carp;
use Bio::EnsEMBL::Utils::RDF qw/feature_uri/;
use Bio::EnsEMBL::Utils::RDF::Mapper;
my %field_callbacks = (version => 'version',
production_name => 'production_name',
id_org_short => 'id_org_short',
lod_uri => 'lod_uri',
type => 'type',
id => 'id',
name => 'name',
description => 'description',
seq_region_name => 'seq_region_name',
cs_name => 'coord_system_name',
cs_version => 'coord_system_version',
start => 'start',
end => 'end',
strand => 'strand',
biotype => 'biotype',
rank => 'rank',
taxon_id => 'taxon_id',
uri => 'uri',
synonyms => 'synonyms',
provenance => 'provenance',
homologues => 'homologues',
xrefs => 'xrefs',
dbname => 'dbname',
homologues => 'homologues',
transcripts => 'transcripts',
exons => 'exons',
translations => 'translations',
protein_features => 'protein_features',
so_term => 'so_term'
);
my %field_callbacks = (
version => 'version',
production_name => 'production_name',
id_org_short => 'id_org_short',
lod_uri => 'lod_uri',
type => 'type',
id => 'id',
name => 'name',
description => 'description',
seq_region_name => 'seq_region_name',
cs_name => 'coord_system_name',
cs_version => 'coord_system_version',
start => 'start',
end => 'end',
strand => 'strand',
biotype => 'biotype',
rank => 'rank',
taxon_id => 'taxon_id',
uri => 'uri',
synonyms => 'synonyms',
provenance => 'provenance',
homologues => 'homologues',
xrefs => 'xrefs',
dbname => 'dbname',
homologues => 'homologues',
transcripts => 'transcripts',
exons => 'exons',
translations => 'translations',
protein_features => 'protein_features',
so_term => 'so_term'
);
=head2 new
......@@ -498,6 +499,12 @@ sub so_term {
my $so_term;
my ($type, $biotype) = ($self->type($object), $self->biotype($object));
if (!defined $biotype) {
# warn "Could not find biotype for SO term mapping\n";
return;
}
eval {
if ($type eq 'gene') {
$so_term = $self->biotype_mapper->gene_biotype_to_name($biotype);
......
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