ShaKer

Usage

import shaker.rna_tools.rna_io as rio
import shaker.simushape as sim

#  Train a model 
data = rio.get_all_data("data/RNA16.react","data/RNA16.dbn") 
model  = sim.make_model(data,data.keys())

# Predict 
print (sim.predict(model,"AAAAAAGGGGCCCCCCCGGGGGUUUUUU"))

To train a simple model you can also type 'shaker' in your commandline and look at the instructions.

Installation

# get vienna RNA binaries via conda or their ppa:
# https://repo.anaconda.com/miniconda/Miniconda2-latest-Linux-x86_64.sh
#conda config --add channels defaults
#conda config --add channels bioconda
#conda config --add channels conda-forge

conda install viennarna
pip install shaker-rna

Mustoe data set

www.chem.unc.edu/rna/data-files/mustoe_2018_DATA_SOFTWARE.zip 

We added this data in shaker readable format unter /data/weeks194_orig/

Notebooks

outdated