ribolands - kinetic analysis of nucleic acids

ribolands is a Python wrapper for multiple nucleic acid kinetic analysis programs, currently Kinfold, RNAsubopt, barriers and treekin. Those programs have to installed separately.

⚠️ Dear users of the cotranscriptional folding simulator DrTransformer, this package provided only a preliminary version of the software which now has been removed. The newest version of DrTransformer is not publicly available yet, but feel free to reach out for beta-testing. Also, the executable for the cotranscriptional folding software BarMap has been removed (since it is has never been officially released). BarMap can be coded with minimal effort using the ribolands package, feel free to reach out if you need help.

Dependencies

ribolands uses RNAsubopt from the ViennaRNA package, as well as barriers and treekin for landscape computations. Make sure that you have recent versions installed:

• ViennaRNA>=v2.4.13
• treekin>=v0.5.1
• barriers>=v1.8.1

Installation

  ~$ python setup.py install
  ~$ python -m pytest tests/ -v -s

Latest changes

• removed DrTransformer, which will be available soon as a separate python package.
• removed all other executables in order to focus on library development.
• lot's of interface changes to build workflows (work in progress)
• next release (v0.10) planned for early 2022

License

MIT