/pyRNAfold

An exploratory project to implement RNAtips algorithm using pandas

Primary LanguageJupyter NotebookMIT LicenseMIT

pyRNAfold

Collection of scripts and jupyter notebooks to analyse and visualize the output of RNAfold program from Vienna RNA package.

Setup

Clone the repo:

$ git clone https://github.com/eco32i/pyRNAfold.git

If you want to use python 3 virtualenv (tested on Ubuntu 16.04):

  • Navigate to pyRNAfold/scripts and run the bootstrap.sh script that will install system wide dependencies and create Python 3 virtual environment called pyRNA in $HOME/.venv:

    $ ./bootstrap.sh --all

    The list of installed packages in the final virtualenv is given in requirements.txt file.

Alternatively, you can use conda to create an environment with the same dependencies.

To run the notebooks, activate pyRNA environment:

$ source ~/.venv/pyRNA/bin/activate

Or, if you are using conda environment:

$ source activate pyRNA

Then go to notebooks directory and start jupyter session:

$ jupyter notebook

Notebooks (HSR1 is used throughout as an example)

  • Folding: explains the output of RNAfold and how it is parsed
  • Folding analysis: an example of working with the output of RNAfold for different temperatures
  • Heatmaps: bokeh heatmaps