[ensembl-dev] gene to coords code issue

Sean O'Keeffe so2346 at columbia.edu
Fri Apr 20 04:49:02 BST 2012

I've used the code below on multiple occasions to convert external gene
names to chromosome coords and it worked fine.
However when I tried it just now I get the error for the very first gene
DNAI2 and the script crashes:

Can't call method "seq_region_name" on unblessed reference

When I tried fetch_by_display_label($id) - I get:

Can't call method "seq_region_name" on an undefined value

Have I missed something?
Thanks for any help,

p.s. I tried connecting to the
useastdb.ensembl.org,<http://useastdb.ensembl.org/>as I'm in the
states, but It gave the following (maybe the 2 issues are

DBI connect('host=useastdb.ensembl.org;port=3306','anonymous',...) failed:
Can't connect to MySQL server on 'useastdb.ensembl.org' (111) at
/home/sean/tools/ensembl_53/modules/Bio/EnsEMBL/Registry.pm line 1329
Can't call method "selectall_arrayref" on an undefined value at
/home/sean/tools/ensembl_53/modules/Bio/EnsEMBL/Registry.pm line 1332.



use strict;
use lib '/home/sean/tools/ensembl_53/modules';

use Bio::SeqIO;
use Bio::Root::IO;
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
 use Bio::EnsEMBL::Registry;

my $registry = 'Bio::EnsEMBL::Registry';
#$registry->load_registry_from_db(-host => 'useastdb.ensembl.org',-user =>
$registry->load_registry_from_db(-host => 'ensembldb.ensembl.org',-user =>

open OUT, ">$gene_file.coords";
for my $geneid ( @unique ) {
    chomp $geneid;
    ($chr,$start, $end) = ensembl_coords($geneid);
    print OUT join("\t", $chr,$start,$end,$geneid),"\n";

sub ensembl_coords {
  my ($id) = @_;

  my $adaptor = $registry->get_adaptor( 'Human', 'Core', 'gene' );

  my $gene = $adaptor->fetch_all_by_external_name($id);
  # my $gene = $adaptor->fetch_by_display_label($id);

  $chr = $gene->seq_region_name();
  $start = $gene->seq_region_start();
  $end = $gene->seq_region_end();
  return ($chr,$start,$end);

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