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

[Brandon Walts]

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.
>
> 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 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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