[ensembl-dev] multiple vega/havana entries
Caffrey, Daniel
Daniel.Caffrey at umassmed.edu
Thu Oct 3 22:36:37 BST 2013
Dear Ensembl developers,
I want to use the API to retrieve havana Ids for ensembl transcripts. I have been using the get_all_DBEntries('Vega_transcript') method. However, I get 2 entries for a single transcript that are essentially identical (They both refer to OTTHUMT00000357449). There are subtle differences (the dbIDs and the display_ids differ, see output below).
My questions:
1) Does anyone know why transcripts are cross-referenced to two havana/vega databases?
2) What is the difference between the two databases (dbID: 669630 and dbID: 669633) and is one more preferable to use than the other?
Thanks for your help!
Daniel
Relevant code snippets:
API Version 73
my @dbEntries = @{ $transcript->get_all_DBEntries('Vega_transcript') };
foreach my $dbEntry(@dbEntries){
my $db=$dbEntry->dbname(); #e.g. Vega_transcript
my $id=$dbEntry->display_id(); # e.g. OTTHUMT00000357450 MAPK14-001
my $primaryId=$dbEntry->primary_id(); # e.g. OTTHUMT00000357450 OTTHUMT00000357449
my $dbType=$dbEntry->type(); #e.g. MISC
my $description=$dbEntry->type(); #this is set to MISC for havana
my $dbDisplayName=$dbEntry->db_display_name(); #e.g. Vega_transcript
my $desc=$dbEntry->description();
my $dbId=$dbEntry->dbID();
print OUT "get_all_DBEntries dbID: $dbId db_display_name: $dbDisplayName dbname: $db primary_id $primaryId displayId: $id type $dbType\n";
}
Output for ENST00000229795 ENSG00000112062
get_all_DBEntries dbID: 669630 db_display_name: Vega transcript dbname: Vega_transcript primary_id OTTHUMT00000357449 displayId: OTTHUMT00000357449 type MISC
get_all_DBEntries dbID: 669633 db_display_name: Vega transcript dbname: Vega_transcript primary_id OTTHUMT00000357449 displayId: MAPK14-001 type MISC
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