Feature request: Download RNA2D schema from R2DT widget
Psirving opened this issue · 4 comments
Hi! First of all, thank you so much for building this tool. The layouts look awesome!
I'm developing a python package to analyze and explore RNA structure data in Jupyter and to create figures for publication: RNAvigate. It includes support for RNA2D data schema files.
Is there a way to obtain these files without installing R2DT locally. If not, could you make this format available via the R2DT widget? Any web-based access option would be helpful.
@Psirving Hi Patrick! Thank you for reaching out, I am actually a big fan of RNAvigate! I saw your RNA Society poster and was very impressed.
It is possible to fetch R2DT results in the RNA 2D JSON Schema format. For example, if you submit a sequence to the R2DT API:
https://www.ebi.ac.uk/Tools/common/tools/help/index.html?tool=r2dt
you get a job id like r2dt-R20230726-220347-0839-95483427-p1m.
Then once the results are ready, the JSON schema file can be fetched like this:
https://www.ebi.ac.uk/Tools/services/rest/r2dt/result/r2dt-R20230726-220347-0839-95483427-p1m/json
This also works for jobs submitted using the R2DT web app at https://rnacentral.org/r2dt as it uses the same API under the hood.
Would this work for you? Thanks again for using R2DT.
Thank you, I'm glad you like RNAvigate! Did we meet at my poster? If I had realized who you were, I would've liked to pick your brain about making a web server for RNAvigate.
This is super helpful and exactly what I was looking for. I think this is the method that I had figured out but forgot how to do. I will include these instructions in the RNAvigate documentation.
A couple of notes:
- I tried to use the sequence from 6AH1 chain A, (B. subtilis subtilis LSU: 6HA1_LSU.txt) but R2DT could not find a matching template. I ended up using this very similar sequence instead: https://rnacentral.org/rna/URS00005C6D29/1052585
- I couldn't find a job ID on that page, so I downloaded the fasta and resubmitted to R2DT.
- A 'Save RNA2D' button in the widget would be a nice feature for a future version. For example, FORNA's download options are SVG, PNG, and JSON (different schema, same idea).
Below is the Linezolid binding site in B. sub LSU mapped by chemical probing:
Thanks Patrick, glad it was helpful!
If I had realized who you were, I would've liked to pick your brain about making a web server for RNAvigate.
Never too late, I am always happy to jump on a call and chat about RNA.
I think this is the method that I had figured out but forgot how to do. I will include these instructions in the RNAvigate documentation.
I will also add this to the R2DT API docs.
I tried to use the sequence from 6AH1 chain A, (B. subtilis subtilis LSU: 6HA1_LSU.txt) but R2DT could not find a matching template
I will investigate why it's not finding a template, thank you for reporting it.
I couldn't find a job ID on that page, so I downloaded the fasta and resubmitted to R2DT
That's the way to go, RNAcentral does not store the 2D schema files at this time.
A 'Save RNA2D' button in the widget would be a nice feature for a future version.
I agree, there should be a Save dropdown menu with several options (the existing SVG and PNG plus an additional JSON option). @blakesweeney @carlosribas What do you think? We would also need an Edit dropdown soon 🤫
Below is the Linezolid binding site in B. sub LSU mapped by chemical probing
Looks very cool! 👏👏👏
Being able to save all the data R2DT can produce would be useful, I will add it to our todo list.