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

[Ramiro Magno]

Thank you Brandon for the information!

On Fri, 13 Sep 2019 at 17:38, Brandon Walts <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
> .
>
>
> 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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