Building RNA Databases with RNAglib

This module (prepare_data) contains all the necessary code to build databases of annotated RNA 3D structures, and the user interfaces with it through the rnaglib_prepare_data command line script. Dataset creation follows the following steps:

  • Fetching the raw RNA structures from either:

  • For each structure, run x3dna-dssr

  • Store x3dna-dssr output in a networkx Graph object

  • If the –annotate flag is passed for pre-training:

    • Chop the whole RNAs into smaller chunks

    • Pre-compute local neighbourhoods

    • Extract all graphlets

Quickstart

Print the help message:

$ rnaglib_prepare_data -h

To run a quick debug build with default values:

$ rnaglib_prepare_data -s structures/ --tag first_build -o builds/ -d

Data versioning

The optional argument –tag is used to name the folder containing the final output. For our distributions we use rnaglib-<’all’ or ‘nr’><’-annotated’ or ‘’><’-chopped’ or ‘’>-<version> depending on the build options. We distribute data builds with all available RNAs and assign all to the tag, and non-redundant structures according to the [BGSU Representative Set](https://www.bgsu.edu/research/rna/databases/non-redundant-list.html). For each of these two choices, we also provide versions pre-processed for [graphlet kernel](https://rnaglib.cs.mcgill.ca/static/docs/html/rnaglib.kernels.html) computations used to compute node similarity and assign the annot value to the tag.

Output

After running the –debug test run above, your ./builds/ folder will contain a single sub-folder called ./builds/graphs with 10 .json files and a file ./builds/graphs/errors.csv. Each of these JSONs contains the annotated RNAs and the CSV contains a list of RNAs that failed to build and the failure reason.

Data building options

  • –nr only outputs RNAs from the non-redundant set from BGSU

  • –chop creates a sub-folder in the build called chops which contains chunked RNAs for even batch sizes

  • –annot builds necessary annotations for computing node similarities