[ensembl-dev] Species metadata file ("assembly" or "assembly_accession" labels) to species ftp paths mapping

[Stefano Giorgetti]

//

Dear Allan,

Thanks for your email and for using Ensembl services.

We have 2 main cases: stand-alone species (for instance all the plants') 
and species sharing a "collection DB" - like bacteria.

For the stand-alone species - say plants - the path to the (release 60) 
GTF would be
http://ftp.ensemblgenomes.org/pub/plants/release-60/gtf/<species>/
where <species> can be found from one of the species metadata files.

For species belonging to a collection - say bacteria - the path to the 
(release 60) GTF would be
http://ftp.ensemblgenomes.org/pub/release-60/bacteria/gtf/<collection>/<species>/
Regrettably, there is no trivial way to get the collection the species 
belongs to.
One hopefully not-too-cumbersome would be to extract it from the 
"core_db" field from the species metadata file.
For instance for "acetobacter_syzygii_gca_002276805", we have core db 
"bacteria_60_collection_core_60_113_1", the collection name would be 
"bacteria_60_collection"; thus giving 
http://ftp.ensemblgenomes.org/pub/release-60/bacteria/gtf/bacteria_60_collection/acetobacter_syzygii_gca_002276805//
/
/
/
Hope it helps.
Any questions, please do not hesitate to ask.

Kind regards,
Stefano on behalf of the Ensembl team/
/
/
/
On 10/07/2025 6:49 am, Allan Kamau wrote:
> Greetings,
>
> Given an entry from one of the species metadata files such as 
> "ftp.ensemblgenomes.org/pub/plants/release-60/species_EnsemblPlants.txt 
> <http://ftp.ensemblgenomes.org/pub/plants/release-60/species_EnsemblPlants.txt>" 
> I would like to determine the ftp path to the "gtf" data of the given 
> species.
>
> Is there such a mapping file or mechanism that I can use?
>
> Or in short if I have an "assembly" value such as "ASM16007v2" or and 
> an "assembly_accession" label for example "GCA_000160075.2" is there a 
> way to determine the ftp path to the gtf data which is 
> "tp.ensemblgenomes.org/pub/release-60/bacteria/gtf/bacteria_118_collection/abiotrophia_defectiva_atcc_49176_gca_000160075 
> <http://tp.ensemblgenomes.org/pub/release-60/bacteria/gtf/bacteria_118_collection/abiotrophia_defectiva_atcc_49176_gca_000160075>" 
> in this case?
>
> Regards,
> - Allan.
>
> _______________________________________________
> Dev mailing listDev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info:https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org
> Ensembl Blog:http://www.ensembl.info/
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20250710/33af2640/attachment.html>