[ensembl-dev] getting sequences from older assemblies using the Perl API

[mag]

Hi Ash,

We do not store dna sequences other than those for the latest available 
assembly version.

We provide some mappings between chromosomes in previous versions and 
the chromosomes from the latest version.
This allows you to map features between assemblies, but not access the 
dna sequence.

If you need the dna sequence for those assemblies, I would recommend 
using the archived version where that assembly was the primary assembly.
For mouse NCBIm37, this would be release 67:
http://may2012.archive.ensembl.org/Mus_musculus/Info/Index

For human GRCh37, this was in release 75:
http://grch37.ensembl.org/Homo_sapiens/Info/Index


Hope that helps,
Magali

On 21/08/2014 07:13, Ashley Waardenberg wrote:
> If I select any other assembly version (below as variable "$version") 
> other than the highest ranked, I seem to only get "N" as sequences 
> returned. I have tried this for both mouse and human. This is using 
> the perl API version 75, below is an example querying a sequence at 
> some specific coordinate. If I retrieve the soft-masked region, it 
> returns lower cases where expected, but is still all "n". If I change 
> the assembly to highest rank (e.g. GRCm38)  it retrieves "proper" 
> sequence, but obviously at the wrong coordinates as I am using NCBIM37 
> fragments.
>
> Is this a possible bug/any ideas?
>
> Ash
>
> #code start
>
> use Bio::EnsEMBL::Registry;
>
>
> my$registry = "Bio::EnsEMBL::Registry";
>
> my $species = "mouse";
>
> my $version = "NCBIM37";
>
>
> $registry->load_registry_from_db(
>
>     -host => 'ensembldb.ensembl.org',
>
>     -user => 'anonymous'
>
> );
>
>
> my $adaptor = $registry->get_adaptor($species,'Core','Slice');
>
> #slice of interest:
>
> my $slice = $adaptor->fetch_by_region('chromosome', 7 , 123336212 , 
> 123338053 , 1, $version);
>
> #different elements of the slice:
>
> my $sequence = $slice->seq();
>
> my $softmasked = $slice->get_repeatmasked_seq( undef, 1 );
>
> my $softmasked_seq = $softmasked->seq();
>
>
> #print sliced sequences:
>
> print $sequence."\n"."\n"."\n";
>
> print $softmasked_seq."\n";
>
> #code end
>
> #this prints the following out:
>
>
> NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
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