From 600f9d5ac8bc1a6dd62170f27526dae1efa62fbb Mon Sep 17 00:00:00 2001
From: Rhoda Kinsella <rhoda@ebi.ac.uk>
Date: Wed, 1 Jun 2011 15:32:15 +0000
Subject: [PATCH] Ian modified code to deal with name change for Corf genes
when there are one to many.
---
.../xref_projection/project_display_xrefs.pl | 17 ++++++++++++-----
1 file changed, 12 insertions(+), 5 deletions(-)
diff --git a/misc-scripts/xref_projection/project_display_xrefs.pl b/misc-scripts/xref_projection/project_display_xrefs.pl
index 9264da5128..9a5f0b715c 100644
--- a/misc-scripts/xref_projection/project_display_xrefs.pl
+++ b/misc-scripts/xref_projection/project_display_xrefs.pl
@@ -13,6 +13,8 @@ use Bio::EnsEMBL::Utils::Eprof qw(eprof_start eprof_end eprof_dump);
my $method_link_type = "ENSEMBL_ORTHOLOGUES";
+my %seen;
+
my ($conf, $registryconf, $version, $compara, $from_species, @to_multi, $print, $names, $go_terms, $delete_names, $delete_go_terms, $no_backup, $full_stats, $descriptions, $release, $no_database, $quiet, $max_genes, $one_to_many, $go_check, $all_sources, $delete_only, $to_species, $from_gene);
GetOptions('conf=s' => \$conf,
@@ -278,7 +280,7 @@ sub project_display_names {
my $from_latin_species = ucfirst(Bio::EnsEMBL::Registry->get_alias($from_species));
# if no display name set, do the projection
- if (check_overwrite_display_xref($to_gene, $from_source, $to_source, $dbEntry)) {
+ if (check_overwrite_display_xref($to_gene, $from_source, $to_source, $dbEntry, $gene_number)) {
if ($dbEntry) {
@@ -626,7 +628,7 @@ sub delete_go_terms {
sub check_overwrite_display_xref {
- my ($to_gene, $from_dbname, $to_dbname, $ref_dbEntry) = @_;
+ my ($to_gene, $from_dbname, $to_dbname, $ref_dbEntry, $gene_number) = @_;
return 1 if (!$to_gene->external_name() && $to_species ne "zebrafish");
@@ -651,9 +653,14 @@ sub check_overwrite_display_xref {
return 1 if ($to_dbname eq "Clone_based_ensembl_gene" or $to_dbname eq "Clone_based_vega_gene");
- if ($ref_dbEntry->display_id =~ /C(\w+)orf(\w+)/){
- $ref_dbEntry->display_id("C".$to_seq_region_name."H".$1."orf".$2);
- return 1;
+ my $name = $ref_dbEntry->display_id;
+ if($seen{$ref_dbEntry->dbID}){
+ $name = $seen{$ref_dbEntry->dbID};
+ }
+ if ( $name =~ /C(\w+)orf(\w+)/){
+ $seen{$ref_dbEntry->dbID} = $name;
+ $ref_dbEntry->display_id("C".$to_seq_region_name."H".$1."orf".$2);
+ return 1;
}
if (!defined ($to_dbEntry) || (($to_dbEntry->display_id =~ /:/) and $to_dbname eq "ZFIN_ID") ){
--
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