sample_fc#

RNAdist.sampling.ed_sampling.sample_fc(fc: RNA.fold_compound, nr_samples: int, undirected: bool = True)#

Samples structures for a sequence and returns pairwise distances of nucleotides

Warning

This function might produce nonsense output if the fc is not set up correctly. If you do not know how to do this consider using sample()

Parameters:

  • fc (RNA.fold_compound) – ViennaRNA fold compound.

  • nr_samples (int) – How many samples should be drawn

  • undirected (bool) – Whether to use undirected or directed Graph to calculate distances

Returns:

N x N matrix

containing approximated expected distances from nucleotide i to j at matrix[i][j]

Return type:

np.ndarray

It is possible to sample expected distances using the ViennaRNA fold compound as follows. Please make sure to enable unique multiloop decomposition via uniq_ML=1.

>>> import RNA
>>> seq = "GGGCUAUUAGCUCAGUUGGUUAGAGCGCACCCCUGAUAAGGGUGAGGUCGCUGAUUCGAAUUCAGCAUAGCCCA"
>>> fc = RNA.fold_compound(seq, RNA.md(uniq_ML=1))
>>> x = sample_fc(fc)
>>> x[0, -1]
2.004000000000001