diff --git a/misc-scripts/xref_projection/project_display_xrefs.pl b/misc-scripts/xref_projection/project_display_xrefs.pl index 627b297fd76387cb836e39c8bc9a605e9dc90352..b01486c57f5b77fbc5b0c5ccada7ab092e3702f5 100644 --- a/misc-scripts/xref_projection/project_display_xrefs.pl +++ b/misc-scripts/xref_projection/project_display_xrefs.pl @@ -11,7 +11,7 @@ use Bio::EnsEMBL::DBSQL::GeneAdaptor; my $method_link_type = "ENSEMBL_ORTHOLOGUES"; -my ($conf, $compara, $from_species, @to_multi, $print, $names, $go_terms, $delete_names, $delete_go_terms, $no_backup, $full_stats, $descriptions, $release, $no_database, $quiet); +my ($conf, $compara, $from_species, @to_multi, $print, $names, $go_terms, $delete_names, $delete_go_terms, $no_backup, $full_stats, $descriptions, $release, $no_database, $quiet, $single_source); GetOptions('conf=s' => \$conf, 'compara=s' => \$compara, @@ -29,6 +29,7 @@ GetOptions('conf=s' => \$conf, 'release=i' => \$release, 'no_database' => \$no_database, 'quiet' => \$quiet, + 'single_source' => \$single_source, 'help' => sub { usage(); exit(0); }); $descriptions = 1; @@ -208,6 +209,8 @@ sub project_display_names { if ($dbEntry) { + next if ($single_source && $dbEntry->dbname() ne $single_source); + # Modify the dbEntry to indicate it's not from this species - set info_type & info_text my $txt = "from $from_latin_species gene " . $from_gene->stable_id(); @@ -599,6 +602,8 @@ sub usage { [--quiet] Don't print percentage progress information to STDOUT. + [--single_source] Specify a single source to project (e.g. HUGO). + [--help] This text. e.g