SEISMIC-RNA

Structure Ensemble Inference by Sequencing, Mutation Identification, and Clustering of RNA

News

Version 0.26 released

SEISMIC-RNA 0.26 adds cofolding of two RNAs, replaces the ensembles step with two separate steps, and shows progress bars while it runs. Output directories from version 0.25 can be read by version 0.26 without migrating, except for output of the ensembles step, which must be regenerated with the two steps that replace it.

New features

  • seismic duplex combines two references into one duplex, and seismic fold then predicts the structure the two molecules form together (cofolding with RNAcofold). A second strand can be another dataset, the same dataset (--dimer, for a homodimer), or a bare sequence with no data (--duplex-file / --duplex-sequence), such as an antisense oligonucleotide.

  • Progress bars now show what SEISMIC-RNA is working on, one line per task, for every parallelized step and for seismic wf as a whole. Hide them with --no-progress (they are hidden automatically with -q or when stderr is not a terminal).

  • seismic collate has been rewritten and now runs by default at the end of seismic wf.

  • seismic filterscan detects domains with a new model based on bridge pairs — the position pairs that link two parts of a domain — tuned with --pair-fdr, --min-fold-change, --detect-fdr, --merge-fdr, and --min-pairs.

  • SEISMIC-RNA starts up faster, and its log messages have been simplified from eight levels to five.

Changes to be aware of

  • The ensembles step has been split into two steps: filterscan (detect domains) and clusterscan (cluster each domain). Its output directory ensembles/ is likewise replaced by filterscan/ and clusterscan/.

  • Graphs are now written only as interactive HTML files. The --svg, --pdf, and --png options have been removed, along with the Kaleido dependency they required; --html / --no-html controls whether each graph is written.

  • The domain-finding options of the old ensembles step (--threshold-divisor, --min-cluster-length, --max-cluster-length, and --gap-mode) have been removed in favor of the new options of filterscan, and --min-pairs now sets the minimum number of bridge pairs per domain.

  • SEISMIC-RNA now requires Python 3.13 (previously 3.11), and its dependencies have been updated to match.

See the changelog for the complete list of changes.

Version 0.25 released — breaking changes require migration

SEISMIC-RNA 0.25 contains several backwards-incompatible changes. Existing output directories produced by version 0.24 cannot be read by version 0.25 without first running the migration command described below.

What changed

  • The relate step has been renamed to IDmut (idmut). Output subdirectories previously named relate/ are now idmut/; file names that began with relate- now begin with idmut-.

  • The mask step has been renamed to Filter (filter). Output subdirectories previously named mask/ are now filter/; file names that began with mask- now begin with filter-.

  • Several command-line options have been renamed or removed. Report JSON fields have been updated to match.

How to migrate

Use seismic migrate to update an existing output directory to the version 0.25 format:

seismic migrate out -o out-new

where out is your old output directory (from version 0.24) and out-new is a new directory that will be created to hold the updated outputs. The original out directory is never modified; if an error occurs the incomplete out-new directory is removed automatically.

Once the command succeeds, verify your results using out-new in place of out for any downstream steps.