[ensembl-dev] Difficulty finding genomic slices using Ensembl Perl API.

[Allan Kamau]

I am trying to obtain sections of sequences (and perhaps accompanying
annotation) of several organisms, for each such request I have the
following pieces of information.
1)species name
2)genome build name
3)chromosome, scaffold or contig name
4)start and end positions
5)orientation of the sequence (fwd or rev)

When I query for the above for some species such as
"anopheles_gambiae" I get no results found in the object
"@db_adaptors" (see below).


use Bio::EnsEMBL::Registry;

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

$registry->load_registry_from_db(
       -host=>'ensembldb.ensembl.org',
       -user=>'anonymous'
);
my @db_adaptors=@{Bio::EnsEMBL::Registry->get_all_DBAdaptors(-species=>"anopheles_gambiae")};

What could I be doing wrong.

The code

$species_name2='Anopheles gambiae';
$species_name_available=$registry->get_alias($species_name2);

returns
"anopheles_gambiae"

Meaning that "anopheles_gambiae" is known to ensembl as a species name
but the outcome of running the preceding code indicates that there are
no db_adaptors for this species.

Is there a graceful way of obtaining the information I am looking for
(which I pointed out in the beginning)?

Allan.