[ensembl-dev] Fetching Age of Base

[Benoit Ballester]

Hi Tom,

Thanks for the prompt reply. 

What would be the description of col4 and col5 ? 

Col4 Hsap-Mfas-Mmul-Ptro  are the species in which the substitution occurred ?
Col5 is a score ? age in Mya?

Thanks 

19	1581102	1581103	Hsap-Mfas-Mmul-Ptro[4]	319	81,81,255
19	1581120	1581121	Hsap-Mfas-Mmul-Ptro[4]	319	81,81,255
19	1581138	1581139	Hsap-Mfas-Mmul-Ptro[4]	319	81,81,255
19	1581150	1581151	Hsap-Ptro[2]	92	23,23,255
19	1581153	1581154	Hsap-Ptro[2]	92	23,23,255
19	1581174	1581175	Hsap-Mfas-Mmul-Ptro[4]	319	81,81,255
19	1581186	1581187	Hsap-Mfas-Mmul-Ptro[4]	319	81,81,255
19	1581189	1581190	Hsap-Mfas-Mmul-Ptro[4]	319	81,81,255
19	1581219	1581220	Hsap-Mfas-Mmul-Ptro[4]	319	81,81,255
19	1581249	1581250	Hsap-Ptro[2]	92	23,23,255
19	1581258	1581259	Hsap-Mfas-Mmul-Ptro[4]	319	81,81,255

--
Benoît Ballester, PhD
INSERM U1090 TAGC
Aix-Marseille-Université
Parc Scientifique de Luminy
13288 Marseille Cedex 9. France

(1st)  benoit.ballester at inserm.fr
(2nd) benoit.ballester at univ-amu.fr
ReMap: http://remap.univ-amu.fr/ 

> On 10 Apr 2024, at 15:50, Thomas Walsh <twalsh at ebi.ac.uk> wrote:
> 
> 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 <mailto:benoit.ballester at inserm.fr>
>> (2nd) benoit.ballester at univ-amu.fr <mailto: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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