Features
This release introduces the essential utilities of SEISMIC-RNA:
- Alignment
- Relation
- Masking
- Clustering
- Tabulation
- Folding*
- Graphing*
*These utilities are implemented for related and masked data, but not yet for clustered data, on which they will fail or produce nonsensical output. This issue will be fixed in a future release.
Caveats
- This target audience of this release is members and collaborators of the Rouskin Lab (i.e. people with whom I already work, who can ask me for all the tech support they wish).
- I have not started writing the documentation meant for end users. So far, I have merely annotated the source code with docstrings and comments. I will add the documentation in future releases.
- Graphing features are very limited so far. The only supported graphs are counts and fractions of mutations per position in a reference sequence, and only from the relate and mask steps. More types of graphs and support for clustering will be added in a future release.
- The relate step is moderately slow. It will be rewritten in C in a future release.
- The table step is very slow. It will be optimized if feasible in a future release.
- The unit tests so far cover only a small fraction of the entire code, with a focus on the relate step, which has the most complicated pure-Python algorithm in the project. That said, my own end-to-end tests have revealed no significant bugs in the current release.
- I do not consider this release to be sufficiently complete, documented, or tested to share with researchers outside of the Rouskin Lab.