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

[Ramiro Magno]

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> wrote:

> 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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