SEISMIC-RNA

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

News

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.