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

[Ramiro Magno]

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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