Commit 5f353122 authored by Kieron Taylor's avatar Kieron Taylor 😠
Browse files

Fixed an inappropriate method of getting species aliases and changed a couple...

Fixed an inappropriate method of getting species aliases and changed a couple of lines to be more direct.
parent 6ebe1736
......@@ -217,15 +217,9 @@ foreach my $local_to_species (@to_multi) {
delete_names($to_ga) if ($delete_names);
delete_go_terms($to_ga) if ($delete_go_terms);
# get taxonomy ids from core databases
my $meta_container = Bio::EnsEMBL::Registry->get_adaptor($from_species, 'Core', 'MetaContainer');
my $from_taxon_id = $meta_container->get_taxonomy_id();
$meta_container = Bio::EnsEMBL::Registry->get_adaptor($to_species, 'Core', 'MetaContainer');
my $to_taxon_id = $meta_container->get_taxonomy_id();
# build Compara GenomeDB objects
my $from_GenomeDB = $gdba->fetch_by_taxon_id($from_taxon_id);
my $to_GenomeDB = $gdba->fetch_by_taxon_id($to_taxon_id);
my $from_GenomeDB = $gdba->fetch_by_registry_name($from_species);
my $to_GenomeDB = $gdba->fetch_by_registry_name($to_species);
my $mlss = $mlssa->fetch_by_method_link_type_GenomeDBs($method_link_type, [$from_GenomeDB, $to_GenomeDB]);
......@@ -838,8 +832,7 @@ sub fetch_homologies {
my ($ha, $mlss, $from_species) = @_;
print "Fetching Compara homologies\n";
my $from_species_alias = lc(Bio::EnsEMBL::Registry->get_alias($from_species));
my $from_species_alias = $gdba->fetch_by_registry_name($from_species)->name();
my %homology_cache;
......
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