This provides a program to compute a, c slices of the RNA polytope using viennaRNA.
This requires the ViennaRNA python package v2.7.0. It comes either from a full install of ViennaRNA or can be installed on its own with pip here.
It also requires numpy and scipy.
The main algorithm is param_partition.py. These are the options:
usage: TL_HPI [-h] [-b B] [--geometry] [--timing] [--unskewed] [--bounds n n n n] [--LP] [-d n]
FASTA_PATH SAVE_PATH
Computes a,c slice for an RNA polytope
positional arguments:
FASTA_PATH Path to fasta file.
SAVE_PATH Directory to save output files.
options:
-h, --help show this help message and exit
-b B b value for computation. Default 0.
--geometry Save geometry of regions as SAVE_PATH/seqname_geometry.txt.
--timing Save timing data as SAVE_PATH/seqname_timing.txt
--unskewed Compute in unskewed space (i.e. excess branching)
--bounds n n n n Integer bounds in dckals/mol for slice in format a_min a_max c_min c_max. Default a>=0 plane (i.e. 0, 10000, -10000, 10000).
--LP Compute without --noLP option in viennaRNA.
-d n Set dandle mode (1 or 2).
By default param_partition will save a file seqname_sig_structs.txt consiting of all the signatures and corresponding structures found within the designated frame.
Adding --geometry and --timing saves additional files. For instance,
python param_partition.py path/to/RNASEQ.fasta save/files/here --geometry --timing
will compute the a,c slice of the a >= plane and save files save/files/here/RNASEQ_geometry.txt, save/files/here/RNASEQ_timing.txt, and the default save/files/here/RNASEQ_sig_structs.txt
The directory partition_algo_testing contains the runTL2ggb.sage file which uses sagemath to create geogebra files for visualizing the computed partiton.