v1.5-beta

April 2021 Update

v 1.5 beta, April 2021

FEATURE CHANGES

New option --stats-opts="..." allows to pass options to the automatic run of statistics.py (when -s is used)
Removed support for 3'->5' Rfam hits, they are now completely ignored. They concern the opposite strand, which is unresolved in 3D.
Removed PyDCA, which is outdated and introduces dependencies conflicts. Code may be adapted later.
A new column in align_column table, index_small_ali, gives the index of the nucléotide in the "3d only" alignment.
3D distance matrices are now computed only for match positions (match to the covariance model)

Corrected a bug which skipped angle conversions from degrees (DSSR) to radians if nucleotides where renumbered.

Khodor Hannoush joins the development of RNANet.

SINA is now used only if you pass the option --sina, Infernal is used by default even for rRNAs.
A new option --cmalign-opts="..." allows to customize your cmalign runs, e.g. with --cyk. The default is no option.
RNANet makes use of PyDCA to compute DCA-related features on the alignments (descriptions to come in the Database.md)
statistics.py now fully supports the computation of 3D distance matrices, with average and standard deviation by RNA family
Now RNANet considers only the equivalence class representative structure by default. To consider all members of an equivalence class (like before), use the --redundant option.

cmalign is not run with --cyk anymore by default, and now requires huge amounts of RAM if launched with the default options.
Moving to a 60-core/128GB server for our internal runs.