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

[Ashley Waardenberg]

Thanks Magali,

If that is the case I will just get the chromosomes and query locally. Could I suggest that the API documentation is updated to reflect this/make it clearer? I.e. In "fetch_by_region" it appears that sequences can be downloaded specific to a coordinate system by including the version of the coordinate system.

Ash

From: mag <mr6 at ebi.ac.uk<mailto:mr6 at ebi.ac.uk>>
Reply-To: Ensembl developers list <dev at ensembl.org<mailto:dev at ensembl.org>>
Date: Thursday, 21 August 2014 6:14 PM
To: Ensembl developers list <dev at ensembl.org<mailto:dev at ensembl.org>>
Subject: Re: [ensembl-dev] getting sequences from older assemblies using the Perl API

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:


NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN



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