Anton Petrov
Anton Petrov
The idea is to run [RNArtist](https://github.com/fjossinet/RNArtistCore) on Rfam families, get [JSON output](https://raw.githubusercontent.com/fjossinet/RNArtist/master/RNArtist/samples/projects/1u6b.json), convert it into R2DT templates and then anytime anyone tries to visualise a sequence from that Rfam family,...
[Typer](https://typer.tiangolo.com) and [rich](https://rich.readthedocs.io/en/stable/) can help improve R2DT CLI interface and console output.
The [code that generates thumbnail images](https://github.com/RNAcentral/R2DT/blob/cd77ed21e75d27263be0a99072b1bcbe7e49825c/utils/shared.py#L421) works well but the images sometimes have jagged edges and the lines are not very smooth ([example](https://rnacentral.org/api/v1/rna/URS0000162127/2d/svg/)). It is desirable to improve the images...
A new version of traveler (https://github.com/cusbg/traveler/commit/b0d69bc64f507fecb7da05b9cf747eb962e97f58) fixes an issue in R2DT where data layers did not work for residues with a label like `NaN`.
Some sequences should not be filtered out based on the presence of the `MultipleHits` warning generated by ribotyper. I am investigating using bit scores as an additional signal to use...
Reduce the number of spawned processes and use Python API instead for tasks like deleting files, unzipping, or wget.
The ribovore team is working on a prototype.
- [x] Make sure all tests pass - [x] Upload precomputed library to the EBI FTP - [x] Update version info in Readme and shared.py - [x] Merge pull request...
It would be useful to establish an integration with [RNAFramework](https://github.com/dincarnato/RNAFramework) so that R2DT can be used to display the secondary structure and reactivities produced by RNAFramework. R2DT should read RNAFramework's...
As pointed out by @pzhaojohnson the model name is not propagated to the json schema output file but it should, and there is a [corresponding field](https://github.com/LDWLab/RNA2D-data-schema/blob/main/example.JSON#L4) in the RNA 2D...