[ensembl-dev] List endpoint for assemblies by species only returns a single assembly

[Kurt Wheeler]

Hi Kieron!

Thanks for getting back to me so quickly. The info/species endpoint does in
fact have what I'm looking for! I can use it to get all the assemblies for
species/strain.

Ultimately what I'm trying to do is download a file like
ftp://ftp.ensemblgenomes.org/pub/release-45/bacteria/fasta/bacteria_100_collection/pseudomonas_aeruginosa_gca_001180445/dna/Pseudomonas_aeruginosa_gca_001180445.E1_London_17_VIM_2_02_09.dna.toplevel.fa.gz
given a species/strain/assembly version. I think that assemblies endpoint
has all the information I need to construct that URL, except for the
`bacteria_100_collection` part. Do you know where I can figure out which
collection a particular organism/strain/assembly version would fall in?
Even better would be if I could get that direct link without having to
construct it.

If you can help with that I appreciate it, but if not I'm still grateful
for the help with the assemblies endpoint!

- Kurt

On Thu, Dec 19, 2019 at 11:49 AM Kieron Taylor <ktaylor at ebi.ac.uk> wrote:

> Hi Kurt,
>
> I believe this is a leakage of our internal understanding, combined with
> poor wording that makes it confusing.
>
> In the human example you can see five "coord_system_versions". This means
> we have assembly mappings from the latest to the previous ones listed.
> These additional assemblies are generally only available in the context of
> the newest assembly, rather than in isolation. The exception to this is the
> long time favourite GRCh37/hg19, and we provide a data freeze of that
> assembly via the grch37.rest.ensembl.org service.
>
> Due to complicated historic reasons, organisms like Pseuodmoniae are
> bundled up differently, such as Pseudomonas_aeruginosa_gca_000705235 :
>
> http://rest.ensembl.org/info/assembly/Pseudomonas_aeruginosa_gca_000705235?content-type=application/json
>
> Here you can see one assembly named "pseuodomonas" attached to the
> "species".
>
> If you want to see what others we have, you need the info/species
> endpoint, but that is very large for bacteria!
>
>
> https://rest.ensembl.org/info/species?content-type=application/json&division=EnsemblBacteria
>
> We are aware that this requires rather more insight into Ensembl's
> historic workings than should be necessary, and we are working to improve
> matters! I have created a ticket to improve the documentation on the
> endpoint in question, but it is a much larger job to have the endpoints
> working the way you would perhaps like them to.
>
>
> Regards,
>
> Kieron
>
>
> Kieron Taylor PhD.
> Ensembl Developer
>
> EMBL, European Bioinformatics Institute
>
>
>
>
>
>
> > On 19 Dec 2019, at 15:22, Kurt Wheeler <kurt.wheeler91 at gmail.com> wrote:
> >
> > Hello,
> >
> > I'm confused by this endpoint:
> http://rest.ensembl.org/documentation/info/assembly_info
> >
> > It says that it will "List the currently available assemblies for a
> species, along with toplevel sequences, chromosomes and cytogenetic bands."
> >
> > However the response only has a single assembly, it's not even with a
> JSON list: []
> >
> > Example:
> http://rest.ensembl.org/info/assembly/PSEUDOMONAS_AERUGINOSA?content-type=application/json
> >
> > Is this a bug? It seems like I should be expecting the response to be a
> list based on the documentation.
> >
> > Thanks,
> >
> > - Kurt
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