arnie

Python API to compute RNA energetics and do structure prediction from all available packages.

Das Lab, 2019

Hannah Wayment-Steele, with inspiration from MWu's wuami_tools

Organization:

examples: example jupyter notebooks with usage.

scripts: scripts for processing sequences in batch.

test: unit tests (still in work)

mea: code for computing Maximum Expected Accuracy structures.

Usage:

Start by creating a file that points to your builds of all the structure prediction packages you wish to use. An example file is provided in example_arnie_file.txt. Create a variable in your .bashrc for this:

export ARNIEFILE="/path/to/arnie/<my_file.txt>"

NB: this file is technically yaml format, but isn't read in by yaml.

See examples/start_here.ipynb for example syntax. In brief, comparing across packages is simple. For computing base pairing probability matrices:

from arnie.bpps import bpps
%pylab inline
example_seq = 'GGGGAAAACCCC'

bpps={}

for pkg in ['vienna','nupack','RNAstructure','contrafold','RNAsoft']:
    bpps[package] = bpps(example_seq, package=pkg)
    
imshow(bpps['vienna'])

Riboswitch fold change:

See examples/riboswitch_fold_change.ipynb for example k_d prediction and fold change prediction.

Coming soon

Help for compiling packages