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

[Ramiro Magno]

Q8: About the assembly mapping endpoint
"map/:species/:asm_one/:region/:asm_two": When a region is not mappable,
the json response is empty. Example:
https://rest.ensembl.org/map/homo_sapiens/GRCh37/1:1..2:1/GRCh38/?coord_system=chromosome;target_coord_system=chromosome

May I suggest to change this behaviour and always return the same
structure, i.e., returning the "original" and "mapped" objects, while
having the start, end, seq_region_name in "original" object with NA or
Null? I am suggesting this because returning an empty response altogether
is ambiguous, in my opinion.

Thanks!

Cheers, RM

On Wed, 11 Sep 2019 at 18:04, Ramiro Magno <ramiro.magno at gmail.com> wrote:

> Q7: What other values than "chromosome" are possible for the optional
> parameters "coord_system" and "target_coord_system"?
>
> On Tue, 10 Sep 2019 at 14:21, Ramiro Magno <ramiro.magno at gmail.com> 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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