[ensembl-dev] Fetching Age of Base

[Thomas Walsh]

Dear Ben,

Age-of-Base is not currently stored in Compara databases, but if you 
have bigBedToBed installed, you can fetch current Age-of-Base data for 
your region of interest as follows:

bigBedToBed 
https://ftp.ensembl.org/pub/data_files/homo_sapiens/GRCh38/compara/Hsap_ages_2072_111.bb 
\
     -chrom=19 -start=1581090 -end=1581269 
Hsap_ages_19_1581091_1581269.bed

The Age-of-Base file is periodically updated, so it may be no harm to 
keep an eye out for updated versions of the file at: 
https://ftp.ensembl.org/pub/data_files/homo_sapiens/GRCh38/compara/

All the best,

Tom Walsh.

On 2024-04-09 16:21, Benoit Ballester wrote:

> Dear Ensembl,
> 
> I am trying to get the "age of base" as described here :
> https://www.ensembl.org/info/genome/compara/age_of_base.html
> 
> Basically, for a slice like this, I'd like to get those "age".
> $slice = $hsap_slice_adaptor->fetch_by_region( 'toplevel', '19' , 
> '1581091','1581269');
> 
> It has been a while since I last used the ensembl API (prob ~v60), so I 
> wonder if I could get those values from a core slice (which I doubt), 
> most likely from a compara object, but which one ? Is this something 
> stored in the compara db for human, or computed on the fly from a 
> multiple alignment objet ?
> 
> The Doxygen doc is not of much of any help for me I am afraid, as I 
> can't get much info there.
> 
> Any embryo of code to get me on track would be must appreciated.
> 
> I am on version 111 of core and compara.
> 
> Thanks,
> Ben
> 
> --
> Benoît Ballester, PhD
> Inserm U1090, TAGC
> Campus de Luminy
> 13288 Marseille Cedex 9
> France
> +33 4 91 82 87 28
> (1st)  benoit.ballester at inserm.fr
> (2nd) benoit.ballester at univ-amu.fr
> ReMap2022: http://remap.univ-amu.fr/
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-- 

Thomas Walsh

Senior Bioinformatician, Ensembl Compara

European Bioinformatics Institute (EMBL-EBI)

Wellcome Genome Campus

Hinxton

Cambridge CB10 1SD

United Kingdom

Email: twalsh at ebi.ac.uk
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