search

fabriziocosta / RaSE-RNA-Structural-Stability-Estimator

RaSE - Rna structurAl Stability Estimator
0 stars 1 forks source link

Graph Context length option #22

Closed mmiladi closed 7 years ago

mmiladi commented 7 years ago

To get a (super) local comparison score between wild and mutant feature graphs: An option to compare and calculate RaSE score on a sub-graph surrounding the SNP location. This option can be implemented to set vector weight(?) of distant locations to zero.

mmiladi commented 7 years ago

Hi @fabriziocosta, Today @martin-mann and I were discussing about the benchmark. The conclusion was without having this locality feature, it would not be a fair comparison of the tools.

fabriziocosta commented 7 years ago

Ok guys, I'll work on it.

fabriziocosta commented 7 years ago

ok, done. the readme still needs to be updated. Note that EDeN has to be updated.

check the notebook for usage. now there is a new parameter: importance_semi_window e.g. print rase.stability_score(0,'A', importance_semi_window=5)

mmiladi commented 7 years ago

Wonderful @fabriziocosta ! Is it a rectangular weight function with a single width option, or a trapezoid one with two window width options?

fabriziocosta commented 7 years ago

in all cases the weights are given as a single rectangular window, inside the window the weight is 1, outside is 0 there are two ways to specify the window:

  1. rase.stability_score(0,'A', importance_semi_window=5) in this way one gives the position, the nt and the semi window around that position to compute the stability score
  2. rase = StructuralStabilityEstimator(seq, k=6, avg_bp_prob_cutoff=0.1, importance_window_begin=2, importance_window_end=12) rase.compute_stability_scores() in this way one gives explicitly the begin and end positions for the window, the stability score is then still computed for all positions