Ensembl Tark Data Provider

[davmlaw]

Andy Yates suggested https://tark.ensembl.org/

This has Ensembl in a format we can use

However, it doesn't have alignments (CIGAR etc) for RefSeq so doesn't handle gaps, have raised issue on project Ensembl/tark#81

So I think we should just do Ensembl to start with

---

Example:

http://tark.ensembl.org/api/transcript/?stable_id=ENST00000256078&stable_id_version=4&expand_all=true

We can get sequence out via:

data["results"][0]["sequence"]["sequence"]

Can get out protein - get_pro_ac_for_tx_ac:

t = data["results"][0]["translations"][0]
In [17]: f'{t["stable_id"]}.{t["stable_id_version"]}'
Out[17]: 'ENSP00000256078.4'

Can implement ``get_tx_for_gene```

http://tark.ensembl.org/api/transcript/search/?identifier_field=KRAS&expand=transcript_release_set%2Cgenes

Can even implement get_tx_for_region via eg:

http://tark.ensembl.org/api/transcript/?loc_start=25362365&loc_end=25403737&loc_region=12&expand_all=false

[davmlaw]

working in branch ensembl_tark

[davmlaw]

ok merged into main. Need to start trying with a test set for a while

Also need to disable RefSeq due to the gap problem

Also need a test for _get_most_recent_release_date

[davmlaw]

Ran TARK using benchmark, 50 out of 50 correct

   count      mean       std       min       25%       50%       75%       max
0   50.0  2.090134  0.460153  1.597495  1.828673  2.057176  2.110917  4.637631
Correct: 50, incorrect: 0, no data: 0, errors: 0

performance is 0.478 / second vs 3/second with cdot REST, so ~6 times slower

Still need the RefSeq check

[davmlaw]

Done initial implementation

[davmlaw]

@holtgrewe - you use Ensembl right? Maybe you'll be interested in this

[holtgrewe]

Thanks

CC @tedil

[davmlaw]

Can use w/no arguments for Ensembl (uses hgvs SeqFetcher for genome sequences) , but for RefSeq or if you want local genome fetching, need to initialise w/special seq fetcher initialised with fasta

from cdot.hgvs.dataproviders.ensembl_tark_data_provider import EnsemblTarkDataProvider, EnsemblTarkSeqFetcher

seqfetcher = EnsemblTarkSeqFetcher(fasta_files=["/data/grch38.fa.gz"]
hdp = EnsemblTarkDataProvider(seqfetcher=seqfetcher)