gtdmmb/rnaprofilingv2

RNAprofiling V2

RNAprofiling takes a sample of RNA secondary structures and produces an interactive webpage summarizing them.

Running tree.py with appropriate options will produce an output\ folder which contains an index.html file and all necessary auxiliary files. This folder can be distributed to anyone to view without any software other than an internet browser.

Users may provide a sample in dot or concatenated ct format. If RNAstructure or ViennaRNA with Python bindings are available locally, the script can use them to generate a sample.

If ViennaRNA is available, you may run

python3 tree.py sequence.fasta.

For RNAstructure sampling use

python3 tree.py --RNAstructure_location /path/to/rnastructure sequence.fasta.

To provide a pregenerated sample in dot format

python3 tree.py --sample_file /path/to/sample.dot --sample_format dot sequence.fasta.

This code has required dependencies on the numpy, networkx, matplotlib, and pygraphviz python libraries. It has been tested with numpy 1.19.5, networkx 2.4, matplotlib 3.3.4, pygraphviz 1.6, and python 3.6.9. It also requires an installation of graphviz to generate the output diagrams.

There is an optional dependency on the RNAlib (Vienna) python bindings. If the are not installed, the code requires either a pregenerated sample or an install of RNAstructure in order to run. RNAlib 2.5.1 or newer must be installed for seeds to work while using its sampling.

To run this code without installing it locally visit https://rnaprofiling.gatech.edu/.

Citation information coming soon.