[ensembl-dev] (v80) "RefSeq_gene_name" DBLink missing for ACKR1?
Luke Goodsell
Luke.Goodsell at ogt.com
Tue Jul 21 10:15:12 BST 2015
Hi EnsEMBL Devs,
Querying an external transcript adaptor for 'NM_002036.3' or 'NM_001122951.2' (transcripts of ACKR1/DARC) and calling get_all_DBEntries or get_all_DBLinks on either the returned transcript or the transcripts' gene objects returns nothing in v80, but in v75 it returns the expected RefSeq_gene_name links.
Have the DBLinks/Entries been intentionally removed, is this in error, or have I missed something?
Example code below.
Kind regards,
Luke
#!/usr/bin/perl
use strict;
use warnings;
use Bio::EnsEMBL::Registry;
my $registry = 'Bio::EnsEMBL::Registry';
$registry->load_registry_from_db(
-host => 'ensembldb.ensembl.org',
-user => 'anonymous',
);
my $external_transcript_adaptor = $registry->get_adaptor( 'Human', 'otherfeatures', 'Transcript' );
foreach my $query ('NM_002036.3', 'NM_001122951.2') {
print "q: " . $query . "\n";
my $transcript = $external_transcript_adaptor->fetch_by_stable_id($query);
print " t: " . $transcript->stable_id . "\n";
foreach my $dbe (
@{ $transcript->get_Gene->get_all_DBEntries() },
@{ $transcript->get_all_DBEntries() },
@{ $transcript->get_Gene->get_all_DBLinks() },
@{ $transcript->get_all_DBLinks() }
) {
printf " XREF %s (%s)\n", $dbe->display_id(), $dbe->dbname();
}
}
-------------- next part --------------
A non-text attachment was scrubbed...
Name: winmail.dat
Type: application/ms-tnef
Size: 10111 bytes
Desc: not available
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20150721/a82a109b/attachment.bin>
More information about the Dev
mailing list