Seismic-rna

New Features

- Join sections (horizontally) from Mask or Cluster reports using new command `seismic join`.

**Full Changelog**: https://github.com/rouskinlab/seismic-rna/compare/v0.12.2...v0.13.0

New Features

- The new command `seismic +delclust` deletes clusters of order higher than a maximum you specify.

Removed Features

- For consistency with the other commands (especially with `--force`), `+addclust` and `+delclust` no longer make backups. This feature will probably be reimplemented in a future update that causes all commands to write to a temporary directory first before moving all files to the output directory; but this priority is low, since SEISMIC-RNA has worked well enough without this safety feature.

**Full Changelog**: https://github.com/rouskinlab/seismic-rna/compare/v0.12.1...v0.12.2

CLI changes

- `+clustup` has been renamed to `+addclust` to make its purpose more obvious.

New Features

- `+addclust` now makes a temporary backup of every file in a clustering directory before modifying the existing files (batches, counts, and report). If a fatal error occurs while modifying the existing files, then the original files are restored from the backup. Without this feature, the original data could be corrupted and rendered unusable.

**Full Changelog**: https://github.com/rouskinlab/seismic-rna/compare/v0.12.0...v0.12.1

New Features

- New command `seismic +clustup` ("cluster update") lets you increase the number of clusters in a clustered dataset _after_ you have already run clustering.
- This feature is most useful if you want to check if clustering works with a small number of clusters (e.g. 2) and then try with more clusters (without needing to rerun clustering with 2 clusters).
- Only the new clusters run; previously run clusters are kept, saving time and energy.
- New clusters are simply appended to the report, the batches, and the counts file, as if you had run clustering with that number of clusters initially.
- There is no limit (beyond computer resources) to the number of clusters you can add, or to the number of times you can run `seismic +clustup` on the same dataset.

Bug Fixes

- Fixed bug where NaNs would not be removed properly when calculating normalized RMSDs.

**Full Changelog**: https://github.com/rouskinlab/seismic-rna/compare/v0.11.5...v0.12.0

New Features
- Cluster reports now include two more fields to indicate the reproducibility of clustering: "NRMSD Between Runs" and "Correlation Between Runs". The nonfunctional "Variation of Information" field has been removed.
- Pool now includes a safeguard to prevent accidentally overwriting Relate reports.

**Full Changelog**: https://github.com/rouskinlab/seismic-rna/compare/v0.11.4...v0.11.5

New Features

- You can now produce ROC and rolling AUC-ROC graphs compared against arbitrary folded sections using `--struct-sect {section}`. Previously, if you didn't provide an explicit CT file, you were obligated to use the folded section that was the same as the section from which the data came.
- The option for the explicit CT file has been renamed from `--structs` to `--struct-file`.

**Full Changelog**: https://github.com/rouskinlab/seismic-rna/compare/v0.11.3...v0.11.4