[ensembl-dev] No chromosomes in API for latest bos taurus

[Simon Andrews]

Something odd is happening in the API for the latest bos Taurus release.  When I try to get chromosome adapters I can't find any.

This worked OK for the previous build and still works OK for other species in the current release.  The web site still shows it as a chromosome based assembly so I'm guessing something is wrong somewhere.

I've put a test script at the bottom - if someone could take a look at this I'd be grateful.

Thanks

Simon.

#!/usr/bin/perl
use warnings;
use strict;
use Bio::EnsEMBL::Registry;

my $registry = 'Bio::EnsEMBL::Registry';

$registry->load_registry_from_db(
    -host => 'ensembldb.ensembl.org',
    -user => 'anonymous'
    );

my $db_adapter = $registry -> get_DBAdaptor("bos taurus","Core");
#my $db_adapter = $registry -> get_DBAdaptor("mus musculus","Core");

warn "Genome is ", $db_adapter->species(), "\n";

my @chr_slices = @{$db_adapter -> get_adaptor('slice') -> fetch_all('chromosome',undef,0,1)};

warn "Found ", scalar @chr_slices, " chromosomes for ", $db_adapter->species(), "\n";
The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT Registered Charity No. 1053902.
The information transmitted in this email is directed only to the addressee. If you received this in error, please contact the sender and delete this email from your system. The contents of this e-mail are the views of the sender and do not necessarily represent the views of the Babraham Institute. Full conditions at: www.babraham.ac.uk<http://www.babraham.ac.uk/terms>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20190121/4739341f/attachment.html>