RNAtweaks

Installation

In addition to the RNAtweaks package you also need the viennarna package from anaconda

pip install RNAtweaks
conda install viennarna

Usage

RNAplfold

For RNAplfold usage two different wrappers exist. One uses the command line version of RNAplfold and the other uses the ViennaRNA API

import RNAtweaks.RNAtweaks as RNAtweaks
sequence = "AAATTTTGGGGGGCCCC"
window = 3  # winsize option of RNAplfold
span = 3   # span option of RNAplfold
region = 3  # ulength option of RNAplfold
constraint = ("paired", 3, 5)
api_result = RNAtweaks.api_rnaplfold(sequence, window, span, region=region, temperature=37.0, constraint=[constraint])
cmd_result = RNAtweaks.cmd_rnaplfold(sequence, window, span, region=region, temperature=37.0, constraint=[constraint])

For now only paired and unpaired constraints are supported. The constraints must be a list of Tuples in the format ("paired"/"unpaired", start, end) in contrast to the ViennaRNA constraints these are zero based. Both calls will produce an identical PLFoldOutput object that reflects the ViennaRNA _lunp file.

PLFoldOutput

Object that reflects the ViennaRNA _lunp file. The objects supports various functions to get different representations of the file. The recommended usage is to produce an numpy array as follows:

array = api_result.numpy_array

However, it is also possible to get the text representation of the file, which is usually produced by RNAplfold via:

array = api_result.get_text(nan="NA", truncated=False)

Hereby nan replaced the non float values with "NA" and the truncated flag is used to either keep or drop the header lines beginning with "#".