Sampling

You can use Boltzmann sampling to approximate expected distances using either the Command Line Interface or the Python API

Python API

The Python API is fully compatible with the ViennaRNA Python fold compound. Thus, you can set up a fold compound and use the sample_fc() function to get a numpy array containing all pairwise distances. Have look into the function documentation for details and examples. If you are only interested in the distance between two nucleotides i and j, you can speed up this procedure by using sample_distance_ij().

Command Line Interface

For approximation via the CLI you need a FASTA file with your sequences in it. This is passed via the --input flag. The File specified in --output will contain a pickled python dictionary with the FASTA identifiers as keys and numpy arrays containing all pairwise expected distances as values.

RNAdist sample --input FASTA --output OUTPUT --num_threads 2 --nr_samples 1000

In contrast to the Python API it does not support constraint folding. To see the documentation of how to visualize the output and further CLI flagst have a look into the CLI documentation RNAdist Command Line Interface.