[ensembl-dev] Ensembl REST API | GET map/cdna/:id/:region

[Ameya Chaubal]

Hi Ramiro,

Thanks for the follow-up. Here are couple of thoughts on your queries:


Q8) This is more of a generic and larger request which could potentially lead to re-looking at most of the end-points. e.g.: Going by REST standards, a correct http code needs to be sent with each response. So this might be looked at a later stage.
Q7) There are couple of  options to get this data:

- Using REST endpoint: http://rest.ensembl.org/info/assembly/homo_sapiens?content-type=application/json <http://rest.ensembl.org/info/assembly/homo_sapiens?content-type=application/json>
The top_level_region key has a list of coord_system which needs to be made unique

- Use Perl API:
Refer to the script given under ‘Coordinate Systems & Slices’ over here : https://www.ebi.ac.uk/training/online/sites/ebi.ac.uk.training.online/files/u1218/Core3.pdf <https://www.ebi.ac.uk/training/online/sites/ebi.ac.uk.training.online/files/u1218/Core3.pdf>

- Use the read only connection to the database and get it from 'coord_system' table

Thanks,
Ameya


> On 24 Sep 2019, at 10:18, Ramiro Magno <ramiro.magno at gmail.com> wrote:
> 
> Hi Devs,
> 
> When can I expect an update on these questions (Q7 and Q8)?
> 
> Thanks a lot!
> 
> Cheers, RM
> 
> On Fri, 13 Sep 2019 at 17:53, Ramiro Magno <ramiro.magno at gmail.com <mailto:ramiro.magno at gmail.com>> wrote:
> Thank you Brandon for the information!
> 
> On Fri, 13 Sep 2019 at 17:38, Brandon Walts <bwalts at ebi.ac.uk <mailto:bwalts at ebi.ac.uk>> wrote:
> Hi Ramiro
> 
> Apologies for the delay. We have some answers for you now, and more will be forthcoming:
> 
> Q1: This endpoint should work for most species. I have seen the errors that sometimes arise, and we think suspect (but have not confirmed) that there may be a bug in the  TranscriptMapper that supports this in the underlying Perl API. We will look into this further.
> 
> Q2: No, but this is a good suggestion and we will look into possibly implementing this.
> 
> Q3: Yes, only transcript IDs are valid for this endpoint.
> 
> Q4 and Q5: For the first part of your question, basically yes. Gap represents a gap in the sequence. We will look into whether setting the "overrun" to a gap is the desired behaviour, or whether there may be a better way to return a result for a query that goes beyond the end of a transcript.
> 
> Best
> -Brandon
> 
> On 10/09/2019 14:21, Ramiro Magno wrote:
>> Hi Devs,
>> 
>> I have a few questions about the endpoint "map/cdna/:id/:region".
>> 
>> Q1: How can I find what species work with this endpoint?
>> 
>> Q2: Is there a way of specifying the "range" parameter so that it starts at 1 and goes till the end of the cDNA sequence? E.g., 1..end?
>> 
>> Q3: In the doc, the description of the "id" parameter reads "An Ensembl stable ID". But only transcript ids are valid choices, correct? For example, making the nonsensical query with a gene id gives back a not so tidy error: https://rest.ensembl.org/map/cdna/ENSG00000115263/1..1000?content-type=application/json;include_original_region=1 <https://rest.ensembl.org/map/cdna/ENSG00000115263/1..1000?content-type=application/json;include_original_region=1>.
>> 
>> Q4: What is the meaning of the variable "gap" in the json response? Is it gap=0 means exon, and gap=1 un-mappable region? When I exceed the end position of the transcript in the "range" parameter I always get the excess as a region flagged as gap=1.
>> 
>> Q5: When I get an excess region as a result of asking a cDNA sequence that goes beyond the length of transcript, why are the genomic coordinates "start" and "end" reported as if they were in cdna coordinate system? E.g., the request: https://rest.ensembl.org/map/cdna/ENST00000375497/1..1000?content-type=application/json;include_original_region=1 <https://rest.ensembl.org/map/cdna/ENST00000375497/1..1000?content-type=application/json;include_original_region=1> yields a last block whose coordinates are start=800, end=1000 for both coordinate systems: "cdna" and "chromosome". Would it not make more sense to just report NA or Null instead?
>> 
>> Q6: What is the meaning of the "rank" variable in the json output?
>> 
>> Many thanks in advance!
>> 
>> Cheers, Ramiro
>> 
>> 
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